Gene expression in biological conditions

ABSTRACT

The present invention relates to a method of determining the presence or absence of a biological condition in animal tissue, wherein the expression of genes in normal tissue and tissue from the biological condition is examined and correlated to standards. The invention further relates to the treatment of the biological condition and an assay for determining the condition. More particularly the invention concerns gene expression in epithelial tissue, such as urianry bladder under both normal and abnormal conditions.

This is a U.S. National Phase Application Under 35 USC 371 and applicant claims the benefit of priority of PCT/DK01/00463 filed 12 Jul. 2001, which was published Under PCT Article 21(2) in English and Danish Application No. PA 2000 01020, filed 30 Jun. 2000.

TECHNICAL FIELD OF THE INVENTION

The present invention relates to a method of determining the presence or absence of a biological condition in animal tissue, wherein the expression of genes in normal tissue and tissue from the biological condition is examined and correlated to standards. The invention further relates to the treatment of the biological condition and an assay for determining the condition.

BACKGROUND

The building of large databases containing human genome sequences is the basis for studies of gene expressions in various tissues during normal physiological and pathological conditions. Constantly (constitutively) expressed sequences as well as sequences whose expression is altered during disease processes are important for our understanding of cellular properties, and for the identification of candidate genes for future therapeutic intervention. As the number of known genes and ESTs build up in the databases, array-based simultaneous screening of thousands of genes is necessary to obtain a profile of transcriptional behaviour, and to identify key genes that either alone or in combination with other genes, control various aspects of cellular life. One cellular behaviour that has been a mystery for many years is the malignant behaviour of cancer cells. It is now known that for example defects in DNA repair can lead to cancer but the cancer-creating mechanism in heterozygous individuals is still largely unknown as is the malignant cell's ability to repeat cell cycles to avoid apoptosis to escape the immune system to invade and metastasize and to escape therapy. There are indications in these areas and excellent progress has been made, buth the myriad of genes interacting with each other in a highly complex multidimensional network is making the road to insight long and contorted.

Similar appearing tumors—morphologically, histochemically, microscopically—can be profoundly different. They can have different invasive and metastasizing properties, as well as respond differently to therapy. There is thus a need in the art for methods which distinguish tumors and tissues on factors different than those currently in clinical use.

The malignant transformation from normal tissue to cancer is believed to be a multistep process, in which tumorsuppressor genes, that normally repress cancer growth show reduced gene expression and in which other genes that encode tumor promoting proteins (oncogenes) show an increased expression level. Several tumor suppressor genes have been identified up till now, as e.g. p16, Rb, p53 (Nesrin Özören and Wafik S. El-Deiry, Introduction to cancer genes and growth control, In: DNA alterations in cancer, genetic and epigenetic changes, Eaton publishing, Melanie Ehrlich (ed) p. 1-43, 2000.; and references therein). They are usually identified by their lack of expression or their mutation in cancer tissue.

Other examinations have shown this downregulation of transcripts to be partly due to loss of genomic material (loss of heterozygosity), partly to methylation of promo-torregions, and partly due to unknown factors (Nesrin Özören and Wafik S. El-Deiry, Introduction to cancer genes and growth control, In: DNA alterations in cancer, genetic and epigenetic changes, Eaton publishing, Melanie Ehrlich (ed) p. 1-43, 2000.; and references therein).

Several oncogenes are known, e.g. cyclinD1/PRAD1/BCL1, FGFs, c-MYC, BCL-2 all of which are genes that are amplified in cancer showing an increased level of transcript (Nesrin Özören and Wafik S. El-Deiry, Introduction to cancer genes and growth control, In: DNA alterations in cancer, genetic and epigenetic changes, Eaton publishing, Melanie Ehrlich (ed) p. 1-43, 2000.; and references therein). Many of these genes are related to cell growth and directs the tumor cells to uninhibited growth. Others may be related to tissue degradation as they e.g. encode enzymes that break down the surrounding connective tissue.

SUMMARY OF THE INVENTION

In one aspect the present invention relates to a method of determining the presence or absence of a biological condition in animal tissue comprising

-   -   collecting a sample comprising cells from the tissue and/or         expression products from the cells,     -   assaying a first expression level of at least one gene from a         first gene group, wherein the gene from the first gene group is         selected from genes expressed in normal tissue cells in an         amount higher than expression in biological condition cells,         and/or     -   assaying a second expression level of at least one gene from a         second gene group, wherein the second gene group is selected         from genes expressed in normal tissue cells in an amount lower         than expression in biological condition cells,     -   correlating the first expression level to a standard expression         level for normal tissue, and/or the second expression level to a         standard expression level for biological condition cells to         determine the presence or absence of a biological condition in         the animal tissue.

Animal tissue may be tissue from any animal, preferably from a mammal, such as a horse, a cow, a dog, a cat, and more preferably the tissue is human tissue. The biological condition may be any condition exhibiting gene expression different from normal tissue. In particular the biological condition relates to a malignant or premalignant condition, such as a tumor or cancer.

Furthermore, the invention relates to a method of determining the stage of a biological condition in animal tissue,

-   -   comprising collecting a sample comprising cells from the tissue,     -   assaying the expression of at least a first stage gene from a         first stage gene group and at least a second stage gene from a         second stage gene group, wherein at least one of said genes is         expressed in said first stage of the condition in a higher         amount than in said second stage, and the other gene is         expressed in said first stage of the condition in a lower amount         than in said second stage of the condition,     -   correlating the expression level of the at least two genes to a         standard level of expression determining the stage of the         condition.

Thereby, it is possible to determine the biological condition in more details, such as determination of a stage and/or a grade of a tumor.

The methods above may be used for determining single gene expressions, however the invention also relates to a method of determining an expression pattern of a cell sample, comprising:

-   -   collecting sample comprising bladder cells and/or expression         products from bladder cells,     -   determining the expression level of at least one gene in the         sample, wherein at least one gene belongs to a first group of         genes, said gene from the first gene group being expressed in a         higher amount in normal tissue than in biological condition         cells, and wherein at least one other gene belongs to a second         group of genes, said gene from the second gene group being         expressed in a lower amount in normal tissue than in biological         condition cells, and the difference between the expression level         of the first gene group in normal cells and biological condition         cells being at least two-fold, obtaining an expression pattern         of the bladder cell sample.

Gene expression patterns may rely on one or a few genes, but more preferred gene expression patterns relies on expression from multiple genes, whereby a combined information from several genes is obtained.

Further, the invention relates to a method of determining an expression pattern of a bladder cell sample independent of the proportion of submucosal, muscle, or connective tissue cells present, comprising:

-   -   determining the expression of one or more genes in a sample         comprising cells, wherein the one or more genes exclude genes         which are expressed in the submucosal, muscle, or connective         tissue, whereby a pattern of expression is formed for the sample         which is independent of the proportion of submucosal, muscle, or         connective tissue cells in the sample.

The expression pattern may be used in a method according to this information, and accordingly, the invention also relates to a method of determining the presence or absence of a biological condition in human bladder tissue comprising,

-   -   collecting a sample comprising cells from the tissue,     -   determining an expression pattern of the cells as defined above,     -   correlating the determined expression pattern to a standard         pattern,     -   determining the presence or absence of the biological condition         in said tissue.     -   as well as a method for determining the stage of a biological         condition in animal tissue, comprising     -   collecting a sample comprising cells from the tissue,     -   determining an expression pattern of the cells as defined above,     -   correlating the determined expression, pattern to a standard         pattern,     -   determining the stage of the biological condition is said         tissue.

The invention further relates to a method for reducing cell tumorigenicity or malignancy of a cell, said method comprising

-   contacting a tumor cell with at least one peptide expressed by at     least one gene selected from genes being expressed in an amount at     least two-fold higher in normal cells than the amount expressed in     said tumor cell, or     comprising -   obtaining at least one gene selected from genes being expressed in     an amount at least two-fold higher in normal cells than the amount     expressed in said tumor cell, -   introducing said at least one gene into the tumor cell in a manner     allowing expression of said gene(s), or -   obtaining at least one nucleotide probe capable of hybridising with     at least one gene of a tumor cell, said at least one gene being     selected from genes being expressed in an amount one-fold lower in     normal cells than the amount expressed in said tumor cell, and -   introducing said at least one nucleotide probe into the tumor cell     in a manner allowing the probe to hybridise to the at least one     gene, thereby inhibiting expression of said at least one gene.

In a further aspect the invention relates to a method for producing antibodies against an expression product of a cell from a biological tissue, said method comprising the steps of

-   obtaining expression product(s) from at least one gene said gene     being expressed as defined above, -   immunising a mammal with said expression product(s) obtaining     antibodies against the expression product.

The antibodies produced may be used for producing a pharmaceutical composition. Further, the invention relates to a vaccine capable of eliciting an immune response against at least one expression product from at least one gene said gene being expressed as defined above.

The invention furthermore relates to the use of any of the methods discussed above for producing an assay for diagnosing a biological condition in animal tissue.

Also, the invention relates to the use of a peptide as defined above as an expression product and/or the use of a gene as defined above and/or the use of a probe as defined above for preparation of a pharmaceutical composition for the treatment of a biological condition in animal tissue.

In yet a further aspect the invention relates to an assay for determining the presence or absence of a biological condition in animal tissue, comprising

-   -   at least one first marker capable of detecting a first         expression level of at least one gene from a first gene group,         wherein the gene from the first gene group is selected from         genes expressed in normal tissue cells in an amount higher than         expression in biological condition cells, and/or     -   at least one second marker capable of detecting a second         expression level of at least one gene from a second gene group,         wherein the second gene group is selected from genes expressed         in normal tissue cells in an amount lower than expression in         biological condition cells.

In another aspect the invention relates to an assay for determining an expression pattern of a bladder cell, comprising at least a first marker and and/or a second marker, wherein the first marker is capable of detecting a gene from a first gene group as defined above, and the second marker is capable of detecting a gene from a second gene group as defined above.

DRAWINGS

FIGS. 1-4. Describes genes that were only present (P) in normal urothelium and absent (A) from the other four samples (samples 1, 2, 3, 4, 5 scored as P, A, A, A, A), genes that were present in normal and superficial tumors and absent from the others (PP,AAA) etcetera. These genes could for example encode tumor inhibitors, or stage specific genes.

FIG. 5. Genes that are decreased (D) in tumors compared with normal urothelium (P,D,D,D,D). These could encode tumor inhibitors.

FIG. 6. Genes that are increased >3 fold in all tumor compared to normal. Encode Tumor associated proteins.

FIG. 7. Genes that are scored as PPPPA but decreased in all tumors and finally absent in the most malignant solid tumor.

FIG. 8. Genes that lose expression in the muscle invasive tumors, PPPAA.

FIG. 9. Genes that re lost in slightly invasive tumors, PPAAA

FIG. 10. Genes that are increased in expression level in all tumors, APPPP. Tumor specific genes.

FIG. 11. Genes that are turned on in all invasive tumors, AAPPP.

FIG. 12. Genes that are associated with muscle invasive tumors. AAAPP.

FIG. 13. Genes that identify solid tumors only AAAAP.

FIG. 14. Genes that identify mixed tumors solid/papillom of invasive type. AAAPA.

FIG. 15. Genes that identify T1 tumors. AAPAA

FIG. 16. Genes that identoify superficial tumors APAAA

FIG. 17 shows the absolute level (called average difference) of appr. 18,000 Expressed Sequence Tags.

FIG. 18 shows western blots based on antibodies raised against synthetic peptides selected from the EST sequence.

DETAILED DESCRIPTION OF THE INVENTION

Samples

The samples according to the present invention may be any tissue sample, it is however often preferred to conduct the methods according to the invention on epithelial tissue, such as epithelial tissue from the bladder. In particular the epithelial tissue may be mucosa.

The sample may be obtained by any suitable manner known to the man skilled in the art, such as a biopsy of the tissue, or a superficial sample scraped from the tissue. The sample may be prepared by forming a cell suspension made from the tissue, or by obtaining an extract from the tissue.

In one embodiment it is preferred that the sample comprises substantially only cells from said tissue, such as substantially only cells from mucosa of the bladder.

Biological Condition

The methods according to the invention may be used for determining any biological condition, wherein said condition leads to a change in the expression of at least one gene, and preferably a change in a variety of genes.

Thus, the biological condition may be any malignant or premalignant condition, in particular in bladder, such as a tumor or an adenocarcinoma, a carcinoma, a teratoma, a sarcoma, and/or a lymphoma, and/or carcinoma-in-situ, and/or dysplasia-in-situ.

Single Gene Expression Contra Expression Pattern

The expression level may be determined as single gene approaches, i.e. wherein the determination of expression from one or two or a few genes is conducted. It is preferred that expression from at least one gene from a first (normal) group is determined, said first gene group representing genes being expressed at a higher level in normal tissue, i.e. so-called suppressors, in combination with determination of expression of at least one gene from a second group, said second group representing genes being expressed at a higher level in tissue from the biological condition than in normal tissue, i.e. so-called oncogenes. However, determination of the expression of a single gene whether belonging to the first group or second group is within the scope of the present invention. In this case it is preferred that the single gene is selected among genes having a high change in expression level from normal cells to biological condition cells.

Another approach is determination of an expression pattern from a variety of genes, wherein the determination of the biological condition in the tissue relies on information from a variety of gene expression, i.e. rather on the combination of expressed genes than on the information from single genes.

Bladder Tumors

The following data presented herein relates to bladder tumors, and therefore the description has focused on the gene expression level as one way of identifying genes that lose or gain function in cancer tissue. Genes showing a remarkable downregulation (or complete loss) or upregulation (gene expression gained de novo) of the expression level—measured as the mRNA transcript, during the malignant progression in bladder from normal mucosa through Ta superficial tumors to T1, slightly invasive tumors, to T2, T3 and T4 which have spread to muscle or even further into lymph nodes or other organs are within the scope of the invention, as well as genes gaining importance during the differentiation from normal towards malignancy.

Gene Groups

The present invention relates to a variety of genes identified either by an EST identification number and/or by a gene identification number. Both type of identification numbers relates to identification numbers of UniGene database, NCBI, build 18.

The various genes have been identified using Affymetrix arrays of the following product numbers:

-   HU35K SubA 900 184 -   HU35K SubB 900 185     First Gene Group

The first gene group relates to at least one, such as at least two, for example at least three, such as at least four, such as at least five, such as more than six genes being expressed in normal tissue cells in an amount higher than expression in biological condition cells. The term “normal tissue cells” relates to cells from the same type of tissue that is examined with respect to the biological condition in question. Thus, with respect to bladder tumors, the normal tissue relates to bladder tissue, in particular to normal bladder mucosa.

The first gene group therefore relates to genes being downregulated in tumors, such genes being expected to serve as tumor suppressor genes, and they are of importance as predictive markers for the disease as loss of one or more of these may signal a poor outcome or an aggressive disease course. Furthermore, they may be important targets for therapy as restoring their expression level, e.g. by gene therapy, or substitution with those peptide products or small molecules with a similar biological effect may suppress the malignant growth.

For a bladder tissue sample a gene from the first gene group is preferably selected individually from genes comprising a sequence as identified below by EST

AA131127_at zo16a05.r1 Stratagene colon (#937204) Homo sapiens cDNA clone 587024 5′ similar to SW: CATX_BOVIN P05689 CATHEPSIN;. AA372630_s_at EST84548 Colon adenocarcinoma IV Homo sapiens cDNA 5′ end. AA434329_at zw24g07.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 770268 5′ similar to contains element TAR1 repetitive element;. C01409_s_at HUMGS0008391, Human Gene Signature, 3′-directed cDNA sequence. RC_AA256485_at zr81e12.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 682126 3′. RC_AA290679_at zt19f03.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 713597 3′ similar to TR: E92665 E92665 AP56;. RC_AA429655_at zw71d04.s1 Soares testis NHT Homo sapiens cDNA clone 781639 3′. RC_AA452410_at zx31f03.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 788093 3′. RC_AA461174_at zx70c04.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 796806 3′. RC_AA491463_at ab01d12.s1 Stratagene fetal retina 937202 Homo sapiens cDNA clone 839543 3′. RC_AA025434_at ze84f10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 365707 3′. RC_AA026030_at ze84d01.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 365665 3′ similar to PIR: A48764 A48764 calpain;. RC_AA054321_s_(—) zl68c01.s1 Stratagene colon (#937204) Homo sapiens cDNA at clone 509760 3′. RC_AA099820_at zk87c05.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 489800 3′. RC_AA161043_at zo74g11.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 592676 3′. RC_AA215379_at zr97c07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 683628 3′. RC_H09281_at yl98f11.s1 Homo sapiens cDNA clone 46316 3′. RC_H18836_at ym45d10.s1 Homo sapiens cDNA clone 51262 3′. RC_H52937_at yq76e12.s1 Homo sapiens cDNA clone 201742 3′ similar to gb: J02982 GLYCOPHORIN B PRECURSOR (HUMAN);. RC_H69547_at yr89e02.s1 Homo sapiens cDNA clone 212474 3′. RC_H95039_at yv20a05.s1 Homo sapiens cDNA clone 243248 3′. RC_N21687_at yx63h03.s1 Soares melanocyte 2NbHM Homo sapiens cDNA clone 266453 3′. RC_N54841_at yv73b09.s1 Soares fetal liver spleen 1NFLS Homo sapiens cDNA clone 248345 3′. RC_N59622_at yv74b06.s1 Soares fetal liver spleen 1NFLS Homo sapiens cDNA clone 248435 3′. RC_N66312_at yz38a06.s1 Homo sapiens cDNA clone 285298 3′. RC_N90717_at za90a10.s1 Soares fetal lung NbHL19W Homo sapiens cDNA clone 299802 3′. RC_R22189_at yh26a02.s1 Homo sapiens cDNA clone 130826 3′. RC_R53457_at yg83e10.s1 Homo sapiens cDNA clone 39835 3′. RC_T53389_s_at ya88f04.s1 Homo sapiens cDNA clone 68767 3′. RC_W86375_s_at zh55a02.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 415946 3′. RC_Z38289_at H. sapiens partial cDNA sequence; clone c-05e04. or a sequence as identified below

RC_AA621122_at af34f04.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 1033567 3′. RC_AA129216_at zn84b03.s1 Stratagene lung carcinoma 937218 Homo sapiens cDNA clone 564845 3′. RC_AA133214_s_(—) zk97h05.s1 Soares pregnant at uterus NbHPU Homo sapiens cDNA clone 490809 3′. RC_H99675_at yx35c02.s1 Homo sapiens cDNA clone 263714 3′. RC_R87160_at yq31h10.s1 Homo sapiens cDNA clone 197443 3′. or a sequence as identified below

RC_AA429904_at zw66d03.s1 Soares testis NHT Homo sapiens cDNA clone 781157 3′. or a sequence as identified below

RC_AA460273_at zx67f05.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 796545 3′. RC_AA490930_at aa46e04.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 823998 3′. RC_AA418072_at zv97g08.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 767774 3′. RC_H61476_s_at yr17e08.s1 Homo sapiens cDNA clone 205574 3′. RC_H16209_at yl28d11.s1 Homo sapiens cDNA clone 159573 3′. RC_N93816_at zb63f11.s1 Soares fetal lung NbHL19W Homo sapiens cDNA clone 308301 3′. RC_H17550_at ym41h05.s1 Homo sapiens cDNA clone 50842 3′. RC_N36835_at yy35f02.s1 Homo sapiens cDNA clone 273243 3′. RC_T35289_at EST82492 Homo sapiens cDNA 3′ end similar to None. RC_AA447977_s_(—) zw82e09.s1 Soares testis NHT Homo sapiens cDNA clone at 782728 3′. RC_AA160879_at zo62h06.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 591515 3′. RC_W45051_at zc21g08.s1 Soares senescent fibroblasts NbHSF Homo sapiens cDNA clone 323006 3′. RC_AA040699_at zk48g04.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486102 3′. RC_R63734_at yi15g05.s1 Homo sapiens cDNA clone 139352 3′. RC_T61475_at yc06h08.s1 Homo sapiens cDNA clone 79935 3′. H23847_at yn71d04.r1 Homo sapiens cDNA clone 173863 5′. RC_AA482014_at zu98d05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 746025 3′ similar to TR: G414993 G414993 CENTRIN.;. RC_AA143323_s_(—) zo37d04.s1 Stratagene endothelial cell 937223 Homo sapiens at cDNA clone 589063 3′ similar to gb: M60483_rna1 PROTEIN PHOSPHATASE PP2A-ALPHA, CATALYTIC SUBUNIT (HUMAN);. R55902_at yg92d05.r1 Homo sapiens cDNA clone 41017 5′. RC_AA035638_at zk28a05.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 471824 3′. AA263146_at PMY0511 KG1a Lambda Zap Express cDNA Library Homo sapiens cDNA 5′. RC_W19222_at zb89h05.s1 Soares senescent fibroblasts NbHSF Homo sapiens cDNA clone 310809 3′ similar to contains Alu repetitive element; contains element L1 repetitive element;. RC_AA262276_at zs25f07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 686245 3′. H61361_s_at yu41b03.r1 Homo sapiens cDNA clone 236333 5′. RC_R10657_s_at yf31e11.s1 Homo sapiens cDNA clone 128492 3′. RC_AA227261_at zr22h04.s1 Stratagene NT2 neuronal precursor 937230 Homo sapiens cDNA clone 664183 3′. RC_AA477641_at zu37b12.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 740159 3′. RC_T70596_at yd15f10.s1 Homo sapiens cDNA clone 108331 3′. R31641_at yh69e02.r1 Homo sapiens cDNA clone 135002 5′. RC_N62855_at yz83c04.s1 Homo sapiens cDNA clone 289638 3′. RC_AA279695_at zs92d10.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 704947 3′. RC_H95071_s_at yv20f02.s1 Soares fetal liver spleen 1NFLS Homo sapiens cDNA clone 243291 3′. RC_N54385_at yv39f05.s1 Soares fetal liver spleen 1NFLS Homo sapiens cDNA clone 245121 3′. H15314_at ym28c02.r1 Homo sapiens cDNA clone 49413 5′. RC_AA151435_at zl43h11.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504741 3′. RC_F01568_at H. sapiens partial cDNA sequence; clone c-06g08. or a sequence as identified below

RC_AA451685_at zx44c03.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 789316 3′. RC_W44745_at zb98a11.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 320828 3′. AA482319_f_at ab15c03.r1 Stratagene lung (#937210) Homo sapiens cDNA clone 840868 5′. RC_AA155820_at zo47a08.s1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 590006 3′. H51340_at yo30c06.r1 Homo sapiens cDNA clone 179434 5′. RC_H09594_at yl97b11.s1 Homo sapiens cDNA clone 46276 3′. RC_N29764_at yw91b09.s1 Homo sapiens cDNA clone 259577 3′. R80048_at yi91e08.r1 Homo sapiens cDNA clone 146630 5′. AC000115_cds1_(—) WUGSC: H_GS188P18.1a gene extracted from Human BAC at clone GS188P18 AA203222_at zx56e01.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 446520 5′ similar to contains element MER17 repetitive element;. RC_AA100437_at zn59e02.s1 Stratagene muscle 937209 Homo sapiens cDNA clone 562490 3′. RC_T51990_at yb29e01.s1 Homo sapiens cDNA clone 72600 3′. AA491114_at aa46e04.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 823998 5′. RC_R39869_at yf63b06.s1 Homo sapiens cDNA clone 26725 3′. RC_AA394071_at zt52g01.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 726000 3′ similar to SW: ADG_MOUSE P22892 GAMMA- ADAPTIN;. RC_AA196790_at zq60b06.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA clone 645971 3′. AA465000_s_at zx80b07.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810037 5′. RC_R39923_at yf51d10.s1 Homo sapiens cDNA clone 25662 3′. RC_R91819_at yp99c05.s1 Homo sapiens cDNA clone 195560 3′ similar to contains MER1 repetitive element;. AA484982_at aa39b02.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 815595 5′. AA036900_at zk29e11.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 471980 5′. RC_AA449951_at zx38a10.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 788730 3′. RC_Z40233_at H. sapiens partial cDNA sequence; clone c-1wg05. RC_AA166810_at zo87a05.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 593840 3′. RC_H06746_at yl83h08.s1 Homo sapiens cDNA clone 44847 3′. AA046674_at zf12d12.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 376727 5′. RC_AA450118_at zx42e09.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 789160 3′. RC_AA486410_at ab36b12.s1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842879 3′. RC_AA026417_at ze92g08.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366494 3′. RC_AA125808_at zl29e12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 503374 3′. RC_AA243721_at zr68f11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 668589 3′. RC_AA452131_at zx15d06.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 786539 3′. RC_N29345_at yw85c10.s1 Homo sapiens cDNA clone 259026 3′. RC_Z39191_at H. sapiens partial cDNA sequence; clone c-13c12. RC_AA156187_at zo47c04.s1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 590022 3′ similar to contains Alu repetitive element;. RC_AA157340_at zo42h04.s1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 589591 3′. RC_AA343514_at EST49299 Gall bladder I Homo sapiens cDNA 3′ end. RC_AA482224_f_(—) ab15c03.s1 Stratagene lung (#937210) Homo sapiens cDNA at clone 840868 3′. RC_AA053021_at zl72f02.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 510171 3′. RC_AA279420_at zs85d09.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 704273 3′ similar to TR: G974805 G974805 T08A11.2;. RC_AA477252_at zu29h10.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 739459 3′. RC_N31597_s_at yy20b11.s1 Homo sapiens cDNA clone 271773 3′. U31875_at Human Hep27 protein mRNA, complete cds. RC_F04611_at H. sapiens partial cDNA sequence; clone c-zse11. AA263032_s_at PMY0335 KG1a Lambda Zap Express cDNA Library Homo sapiens cDNA 5′. AA447052_at zw86b06.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 783827 5′ similar to TR: G595950 G595950 PROTEIN N- TERMINAL ASPARAGINE AMIDOHYDROLASE.; RC_AA056247_at zf62c02.s1 Soares retina N2b4HR Homo sapiens cDNA clone 381506 3′ similar to contains Alu repetitive element;. RC_AA156532_at zo34b05.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 588753 3′. RC_AA456039_at aa03d01.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 812161 3′. RC_AA461444_at zx68b01.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 796585 3′. RC_AA033974_at zi05c10.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429906 3′. RC_AA034365_at zf02b10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 375739 3′ similar to gb: J05096_rna1 SODIUM/ POTASSIUM-TRANSPORTING ATPASE ALPHA-1 CHAIN (HUMAN); contains Alu repetitive element;. RC_N22115_s_at yw32a09.s1 Homo sapiens cDNA clone 253912 3′. RC_W04698_at zb94b05.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 320433 3′. AA126592_at zl17g05.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 502232 5′. AA428172 _f_at zw32b06.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 770963 5′. C01790_at HUMGS0003746, Human Gene Signature, 3′-directed cDNA sequence. RC_AA017146_at ze41a07.s1 Soares retina N2b4HR Homo sapiens cDNA clone 361524 3′ similar to contains element PTR7 repetitive element;. RC_AA236037_at zs05g08.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 684350 3′. RC_AA026270_at ze97f07.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366949 3′. RC_AA233837_at zr47f06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 666563 3′. RC_H60595_s_at yr41h02.s1 Homo sapiens cDNA clone 207891 3′. RC_N66388_at yz39f01.s1 Homo sapiens cDNA clone 285433 3′. RC_N91023_at zb41a09.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 306136 3′. RC_W80354_at zh49a02.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 415370 3′. RC_T51995_at yb29e09.s1 Homo sapiens cDNA clone 72616 3′. RC_AA463637_at zx98h04.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 811831 3′. RC_AA161085_at zo62h09.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 591521 3′ similar to SW: PPAP_RAT P20646 PRO- STATIC ACID PHOSPHATASE PRECURSOR;. RC_AA489101_at aa56h11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 824997 3′. RC_AA255464_at zr83b02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 682251 3′. RC_AA609614_at af15f12.s1 Soares testis NHT Homo sapiens cDNA clone 1031759 3′. L32832_s_at Homo sapiens zinc finger homeodomain protein (ATBF1-A) mRNA, complete cds. AA464051_s_at zx86d04.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810631 5′. RC_Z39652_at H. sapiens partial cDNA sequence; clone c-1fg03. AB002321_at Human mRNA for KIAA0323 gene, partial cds. RC_D59981_s_at Human fetal brain cDNA 3′-end GEN-079C04. RC_AA027954_at zk05c12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 469654 3′. RC_AA115559_at zl07b12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491615 3′. L02547_at Homo sapiens (clone pZ50-19) cleavage stimulation factor 50 kDa subunit, complete cds RC_AA256996_at zr81h11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 682149 3′. RC_AA450373_at zx05h06.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 785627 3′. RC_N71875_at yz34f07.s1 Homo sapiens cDNA clone 284965 3′. AA431505_at zw76e03.r1 Soares testis NHT Homo sapiens cDNA clone 782140 5′. U77942_at Human syntaxin 7 mRNA, complete cds. RC_AA393876_s_(—) zv64h10.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA at clone 758467 3′. W16686_at zb08f12.r1 Soares fetal lung NbHL19W Homo sapiens cDNA clone 301487 5′. RC_AA287388_at zs50f04.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 700927 3′. RC_F02397_s_at H. sapiens partial cDNA sequence; clone c-0xh11. AA247679_at hfe0045.seq.F Human fetal heart, Lambda ZAP Express Homo sapiens cDNA 5′. RC_AA282791_at zs91c05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 704840 3′. AA504744_at aa63f03.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 825629 5′. RC_AA149987_at zo03d03.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 566597 3′. RC_AA262485_at zs17h07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 685501 3′. AA436536_at zv08g07.r1 Soares NhHMPu S1 Homo sapiens cDNA clone 753084 5′. RC_AA037828_at zf03g09.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 375904 3′. RC_AA255628_at zs31g06.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 686842 3′. AA418098_at zv94b04.r1 Soares NhHMPu S1 Homo sapiens cDNA clone 767407 5′. RC_N21380_at yx54c04.s1 Homo sapiens cDNA clone 265542 3′. AA459542_s_at zx89d08.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810927 5′ similar to TR: G608025 G608025 ANKYRIN G.;. RC_AA464180_at zx83f04.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810367 3′ similar to gb: M38188 OVARIAN GRANULOSA CELL 13.0 KD PROTEIN HGR74 (HUMAN);. RC_AA143726_at zo67g06.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 591994 3′ similar to TR: G530823 G530823 EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE.;. RC_N38930_at yy43e04.s1 Homo sapiens cDNA clone 274014 3′. H27242_at yl63h11.r1 Homo sapiens cDNA clone 162981 5′ similar to SP: GCN5_YEAST Q03330 TRANSCRIPTIONAL ACTIVATOR;. RC_AA002088_at zh85g03.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 428116 3′. D31313_s_at Human fetal-lung cDNA 5′-end sequence. RC_R40702_at yf73f10.s1 Homo sapiens cDNA clone 27969 3′. RC_AA405543_at zw39c01.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 772416 3′. RC_AA284143_at zs47c07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 700620 3′. RC_AA158234_at zo76b01.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 592777 3′. R66920_at yi25f09.r1 Homo sapiens cDNA clone 140297 5′ similar to contains Alu repetitive element;. RC_AA034189_at zi06h12.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 430055 3′. AA147510_s_at zl50c12.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 505366 5′. RC_N48715_at yy75h02.s1 Homo sapiens cDNA clone 279411 3′. AA489299_at ab35g04.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842838 5′. RC_AA242799_at zr65f06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 668291 3′ similar to SW: SPO8_YEAST P41833 TRANSCRIPTIONAL REGULATOR SPO8. [1];. AA091412_s_at ll2053.seq.F Fetal heart, Lambda ZAP Express Homo sapiens cDNA 5′. RC_H70554_at yr91a03.s1 Homo sapiens cDNA clone 212620 3′. RC_AA256208_at zr80a08.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 681974 3′. RC_R64660_at yi22a10.s1 Homo sapiens cDNA clone 139962 3′. RC_AA135185_at zo27a05.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 588080 3′. AA442428_at zv70f08.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 759015 5′ similar to SW: YB72_YEAST P38137 HYPOTHETICAL 60.5 KD PROTEIN IN PDB1-ABD1 INTERGENIC REGION.;. RC_AA293719_at zt55h03.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 726293 3′. RC_AA287131_at zt20g02.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 713714 3′ similar to TR: E124071 E124071 NAD+− ISOCITRATE DEHYDROGENASE;. AB002387_at Human mRNA for KIAA0389 gene, complete cds. RC_N50550_at yy89f05.s1 Homo sapiens cDNA clone 280737 3′. or a sequence as identified below

RC_AA599501_at ag23g12.s1 Jia bone marrow stroma Homo sapiens cDNA clone 1071238 3′. RC_AA443923_at zv51a02.s1 Soares testis NHT Homo sapiens cDNA clone 757130 3′. R82598_s_at yj19b12.r1 Homo sapiens cDNA clone 149183 5′. or a sequence as identified below

RC_AA402000_at zu55b03.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 741869 3′ similar to TR: G452270 G452270 2-19 PROTEIN PRECURSOR.;. or a sequence as identified below

RC_T40767_at ya11a06.s1 Homo sapiens cDNA clone 61138 3′. RC_AA426454_s_(—) zv61f08.s1 Soares testis at NHT Homo sapiens cDNA clone 758151 3′ similar to contains element TAR1 repetitive element;. RC_AA057620_at zf15h06.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 377051 3′. RC_AA398197_at zt59a08.s1 Soares testis NHT Homo sapiens cDNA clone 726614 3′. RC_N63332_at yz33d11.s1 Homo sapiens cDNA clone 284853 3′ similar to contains Alu repetitive element;. RC_H58692_s_at yr20g08.s1 Homo sapiens cDNA clone 205886 3′ similar to SP: FTDH_RAT P28037 FORMYLTETRAHYDROFOLATE DEHYDROGENASE;. or a sequence as identified below

zo76b01.s1 Stratagene pancreas (#937208) Homo sapiens RC_AA158234_at cDNA clone 592777 3′. yo61a11.s1 Homo sapiens cDNA clone 182396 3′. RC_H42123_at H. sapiens partial cDNA sequence; clone c-13f02. RC_Z39200_at yx63h03.s1 Soares melanocyte 2NbHM Homo sapiens cDNA RC_N21687_at clone 266453 3′. Homo sapiens mRNA for uroplakin II. Y13645_at zb86b03.s1 Soares senescent fibroblasts NbHSF Homo sapiens RC_N98461_at cDNA clone 310445 3′. zd99d10.s1 Soares fetal heart NbHH19W Homo sapiens RC_W92449_at cDNA clone 357619 3′. H. sapiens partial cDNA sequence; clone c-13c12. RC_Z39191_at zl29e12.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA125808_at cDNA clone 503374 3′. ya11a06.s1 Homo sapiens cDNA clone 61138 3′. RC_T40767_at yb29c05.s1 Homo sapiens cDNA clone 72584 3′. RC_T51972_at zs58b06.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA286862_at IMAGE: 701651 3′. yw91b09.s1 Homo sapiens cDNA clone 259577 3′. RC_N29764_at zw32b06.r1 Soares ovary tumor NbHOT Homo sapiens cDNA AA428172_f_at clone 770963 5′. yj35d05.s1 Homo sapiens cDNA clone 150729 3′. RC_H02265_at zb98a11.s1 Soares parathyroid tumor NbHPA Homo sapiens RC_W44745_at cDNA clone 320828 3′. yp99c05.s1 Homo sapiens cDNA clone 195560 3′ similar to RC_R91819_at contains MER1 repetitive element;. zx84d05.r1 Soares ovary tumor NbHOT Homo sapiens cDNA AA464468_at clone 810441 5′. zp78e01.s1 Stratagene HeLa cell s3 937216 Homo sapiens RC_AA188647_at cDNA clone 626328 3′ similar to TR: G998813 G998813 TIF1. [1];. zu57g11.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA405832_at clone 742148 3′ similar to TR: G780241 G780241 AU- BINDING PROTEIN/ENOYL-COA HYDRATASE.;. zc13b12.s1 Soares parathyroid tumor NbHPA Homo sapiens RC_W37778_f_at cDNA clone 322175 3′ similar to contains LTR2.t3 LTR2 repetitive element;. Homo sapiens breast cancer-specific protein 1 (BCSG1) AF010126_at mRNA, complete cds. yx83a05.r1 Homo sapiens cDNA clone 268304 5′. N36432_at zr74c04.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA236533_s_at 669126 3′ similar to gb: S69002 ECOTROPIC VIRUS INTEGRATION 1 SITE PROTEIN (HUMAN);. zt55e05.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA293163_at clone 726272 3′. zq60b06.s1 Stratagene neuroepithelium (#937231) Homo RC_AA196790_at sapiens cDNA clone 645971 3′. zr53g12.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA253220_at 667174 3′. zn59e02.s1 Stratagene muscle 937209 Homo sapiens cDNA RC_AA100437_at clone 562490 3′. zt28d03.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA293300_s_at clone 714437 3′. H. sapiens partial cDNA sequence; clone c-1fg03. RC_Z39652_at Human glutathione transferase M2 (GSTM2) mRNA, complete M63509_s_at cds H. sapiens partial cDNA sequence; clone c-1ke11. RC_Z39842_at yx78e10.s1 Homo sapiens cDNA clone 267882 3′. RC_N23319_at zs78d11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA278817_at IMAGE: 703605 3′. Homo sapiens mRNA in the region near the btk gene involved L20773_at in a-gamma-globulinemia yi44h05.s1 Soares placenta Nb2HP Homo sapiens cDNA RC_R69276_at clone 142137 3′. H. sapiens partial cDNA sequence; clone c-15d02. RC_F02641_at zw03a04.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA424791_at 768174 3′ similar to contains Alu repetitive element;. yf63b06.s1 Homo sapiens cDNA clone 26725 3′. RC_R39869_at ab15c03.s1 Stratagene lung (#937210) Homo sapiens cDNA RC_AA482224_f_at clone 840868 3′. ze76f02.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA025277_at cDNA clone 364923 3′ similar to contains Alu repetitive element; contains element LTR4 repetitive element;. ab15c03.r1 Stratagene lung (#937210) Homo sapiens cDNA AA482319_f_at clone 840868 5′. ze47b04.s1 Soares retina N2b4HR Homo sapiens cDNA clone RC_AA001045_at 362095 3′. zo10f03.s1 Stratagene neuroepithelium NT2RAMI 937234 RC_AA130645_s_at Homo sapiens cDNA clone 567293 3′ similar to SW: NI2M_BOVIN Q02369 NADH-UBIQUINONE OXIDORE- DUCTASE B22 SUBUNIT;. zt37c02.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA291659_at clone 724514 3′. zk72d02.r1 Soares pregnant uterus NbHPU Homo sapiens AA046768_at cDNA clone 488355 5′. yl81e01.r1 Homo sapiens cDNA clone 44466 5′. H07011_at zt54g04.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA293533_i_at clone 726198 3′ similar to gb: J05158 CARBOXYPEPTIDASE N 83 KD CHAIN (HUMAN);. zn63g10.s1 Stratagene HeLa cell s3 937216 Homo sapiens RC_AA100649_at cDNA clone 562914 3′ similar to SW: LCFA_ECOLI P29212 LONG-CHAIN-FATTY-ACID-COA LIGASE;. ze41a07.s1 Soares retina N2b4HR Homo sapiens cDNA clone RC_AA017146_at 361524 3′ similar to contains element PTR7 repetitive element;. zp40g07.s1 Stratagene muscle 937209 Homo sapiens cDNA RC_AA180054_at clone 611964 3′. PMY0335 KG1a Lambda Zap Express cDNA Library Homo AA263032_s_at sapiens cDNA 5′. zd46f07.r1 Soares fetal heart NbHH19W Homo sapiens W69310_at cDNA clone 343717 5′. zr05e02.s1 Stratagene NT2 neuronal precursor 937230 Homo RC_AA219653_at sapiens cDNA clone 650618 3′. aa91c07.s1 Stratagene fetal retina 937202 Homo sapiens RC_AA457235_at cDNA clone 838668 3′. aa16h10.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA455967_at 813475 3′. yx51a09.r1 Homo sapiens cDNA clone 265240 5′. N27670_at za65e02.s1 Homo sapiens cDNA clone 297434 3′. RC_N80152_at yi22a10.s1 Homo sapiens cDNA clone 139962 3′. RC_R64660_at zo64g03.s1 Stratagene pancreas (#937208) Homo sapiens RC_AA147218_s_at cDNA clone 591700 3′. HUMGS0007818, Human Gene Signature, 3′-directed cDNA C01139_at sequence. PMY0691 KG1a Lambda Zap Express cDNA Library Homo AA285284_at sapiens cDNA 5′. zx44c03.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA451685_at cDNA clone 789316 3′. zx56e01.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens AA203222_at cDNA clone 446520 5′ similar to contains element MER17 repetitive element;. zt52g01.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA394071_at clone 726000 3′ similar to SW: ADG_MOUSE P22892 GAMMA- ADAPTIN;. zv17e07.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA479096_at 753924 3′. zo34b05.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA156532_at clone 588753 3′. H. sapiens partial cDNA sequence; clone c-1wg05. RC_Z40233_at seq2490 Homo sapiens cDNA clone 3HFLSK20-87 3′. RC_T03927_at EST186294 Colon carcinoma (HCC) cell line II Homo sapiens AA314457_at cDNA 5′ end. yy89f05.s1 Homo sapiens cDNA clone 280737 3′. RC_N50550_at zp88f04.s1 Stratagene HeLa cell s3 937216 Homo sapiens RC_AA191524_at cDNA clone 627295 3′. yw90b12.s1 Homo sapiens cDNA clone 259487 3′. RC_N29740_at yy75h02.s1 Homo sapiens cDNA clone 279411 3′. RC_N48715_at zx98h04.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA463637_at 811831 3′. zw38a06.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA404487_at cDNA clone 772306 3′. ym26a10.s1 Homo sapiens cDNA clone 49155 3′. RC_H16666_at zv24d11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA406197_at 754581 3′. yl97b11.s1 Homo sapiens cDNA clone 46276 3′. RC_H09594_at zo62h09.s1 Stratagene pancreas (#937208) Homo sapiens RC_AA161085_at cDNA clone 591521 3′ similar to SW: PPAP_RAT P20646 PROSTATIC ACID PHOSPHATASE PRECURSOR;. zx15d06.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA452131_at cDNA clone 786539 3′. zt54g04.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA293533_f_at clone 726198 3′ similar to gb: J05158 CARBOXYPEPTIDASE N 83 KD CHAIN (HUMAN);. zt59a08.s1 Soares testis NHT Homo sapiens cDNA clone RC_AA398197_at 726614 3′. zx86d04.r1 Soares ovary tumor NbHOT Homo sapiens cDNA AA464051_s_at clone 810631 5′. yb29e01.s1 Homo sapiens cDNA clone 72600 3′. RC_T51990_at zr54a11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA236356_at 667196 3′. zd92a04.r1 Soares fetal heart NbHH19W Homo sapiens W92678_at cDNA clone 356910 5′ similar to contains element LTR3 repetitive element;. yz33d11.s1 Homo sapiens cDNA clone 284853 3′ similar to RC_N63332_at contains Alu repetitive element;. Human aorta cDNA 5′-end GEN-259H09. C16281_s_at zu29h10.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA477252_at clone 739459 3′. yw20e07.r1 Homo sapiens cDNA clone 252804 5′. H88035_s_at Human mRNA for KIAA0389 gene, complete cds. AB002387_at yg45h12.s1 Homo sapiens cDNA clone 35838 3′. RC_R45698_at zr75g11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA236542_at 669284 3′. EST89388 Small intestine I Homo sapiens cDNA 5′ end similar AA376875_at to monoamine oxidase A. yg15g06.s1 Homo sapiens cDNA clone 32365 3′. RC_R43365_at yl83h08.s1 Homo sapiens cDNA clone 44847 3′. RC_H06746_at zr47f06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA233837_at 666563 3′. zf15h06.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA057620_at cDNA clone 377051 3′. zx42e09.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA450118_at cDNA clone 789160 3′. ae37b10.s1 Gessler Wilms tumor Homo sapiens cDNA clone RC_AA598872_at 897979 3′. zl52g06.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA147646_s_at cDNA clone 505594 3′. zb94b05.s1 Soares parathyroid tumor NbHPA Homo sapiens RC_W04698_at cDNA clone 320433 3′. yv39c06.s1 Homo sapiens cDNA clone 245098 3′. RC_N54365_at zr80a08.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA256208_at 681974 3′. zk62g01.r1 Soares pregnant uterus NbHPU Homo sapiens AA046593_at cDNA clone 487440 5′. zh85g03.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens RC_AA002088_at cDNA clone 428116 3′. zr81c12.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA256273_at 682102 3′. aa46e04.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone AA491114_at IMAGE: 823998 5′. zt55h03.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA293719_at clone 726293 3′. zl84c04.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA086005_at clone 511302 3′. zw44a07.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA479885_at cDNA clone 772884 3′. zv70f08.r1 Soares total fetus Nb2HF8 9w Homo sapiens AA442428_at cDNA clone 759015 5′ similar to SW: YB72_YEAST P38137 HYPOTHETICAL 60.5 KD PROTEIN IN PDB1-ABD1 INTERGENIC REGION.;. ab36b12.s1 Stratagene HeLa cell s3 937216 Homo sapiens RC_AA486410_at cDNA clone 842879 3′. yf89f02.r1 Homo sapiens cDNA clone 29665 5′. R15268_at zw86a10.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA443658_at cDNA clone 783834 3′ similar to TR: G438639 G438639 LAMIN B RECEPTOR. [1];. ym39b01.s1 Homo sapiens cDNA clone 50559 3′. RC_H16790_at zx80b07.r1 Soares ovary tumor NbHOT Homo sapiens cDNA AA465000_s_at clone 810037 5′. yy43e04.s1 Homo sapiens cDNA clone 274014 3′. RC_N38930_at Human mRNA for KIAA0323 gene, partial cds. AB002321_at H. sapiens partial cDNA sequence; clone c-0qb09. RC_Z38810_at WUGSC: H_GS188P18.1a gene extracted from Human BAC AC000115_cds1_at clone GS188P18 zr83b02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA255464_at 682251 3′. zs31g06.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA255628_at IMAGE: 686842 3′. yr91a03.s1 Homo sapiens cDNA clone 212620 3′. RC_H70554_at EST180743 Jurkat T-cells V Homo sapiens cDNA 5′ end. AA309880_at yg21a08.s1 Homo sapiens cDNA clone 32940 3′. RC_R43812_at zv47a04.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA425636_at clone 756750 3′. yz39f01.s1 Homo sapiens cDNA clone 285433 3′. RC_N66388_at zs85d09.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA279420_at IMAGE: 704273 3′ similar to TR: G974805 G974805 T08A11.2;. zi05c10.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens RC_AA033974_at cDNA clone 429906 3′. Homo sapiens sodium bicarbonate cotransporter (HNBC1) AF007216_at mRNA, complete cds. aa56h11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA489101_at IMAGE: 824997 3′. Human aorta cDNA 5′-end GEN-286G10. D79601_f_at yw70f05.s1 Homo sapiens cDNA clone 257601 3′. RC_N30856_at Homo sapiens clk2 mRNA, complete cds L29218_s_at zo67g06.s1 Stratagene pancreas (#937208) Homo sapiens RC_AA143726_at cDNA clone 591994 3′ similar to TR: G530823 G530823 EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE.;. zl17g05.r1 Soares pregnant uterus NbHPU Homo sapiens AA126592_at cDNA clone 502232 5′. H. sapiens partial cDNA sequence; clone c-0xh11. RC_F02397_s_at zs27d03.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA252765_at IMAGE: 686405 3′. zc36a04.s1 Soares senescent fibroblasts NbHSF Homo sapiens RC_W46846_at cDNA clone 324366 3′. zo27a05.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA135185_at clone 588080 3′. yf73f10.s1 Homo sapiens cDNA clone 27969 3′. RC_R40702_at yv36d12.s1 Homo sapiens cDNA clone 244823 3′. RC_N52565_at zc06a02.s1 Soares parathyroid tumor NbHPA Homo sapiens RC_W32506_s_at cDNA clone 321482 3′. zr85c04.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA255539_at 682470 3′. zx38a10.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA449951_at cDNA clone 788730 3′. cchn2404.seq.F Fetal heart, Lambda ZAP Express Homo AA091278_at sapiens cDNA 5′. zs05g08.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA236037_at IMAGE: 684350 3′. II2053.seq.F Fetal heart, Lambda ZAP Express Homo sapiens AA091412_s_at cDNA 5′. zf12b09.r1 Soares fetal heart NbHH19W Homo sapiens AA046865_at cDNA clone 376697 5′. EST27743 Cerebellum II Homo sapiens cDNA 5′ end. AA324825_at zx79d09.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA454840_s_at clone 809969 3′. zh49a02.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens RC_W80354_at cDNA clone 415370 3′. zt65c03.s1 Soares testis NHT Homo sapiens cDNA clone RC_AA402484_at 727204 3′. 15h10 Human retina cDNA randomly primed sublibrary Homo W26883_at sapiens cDNA. zs17h07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA262485_at IMAGE: 685501 3′. zw39c01.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA405543_at cDNA clone 772416 3′. yx54c04.s1 Homo sapiens cDNA clone 265542 3′. RC_N21380_at zn77a05.s1 Stratagene NT2 neuronal precursor 937230 Homo RC_AA121360_s_at sapiens cDNA clone 564176 3′. Homo sapiens zinc finger homeodomain protein (ATBF1-A) L32832_s_at mRNA, complete cds. Human fetal-lung cDNA 5′-end sequence. D31313_s_at ym45b05.r1 Homo sapiens cDNA clone 51043 5′ similar to H18718_at contains Alu repetitive element;. zf03g09.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA037828_at cDNA clone 375904 3′. yi04c10.s1 Homo sapiens cDNA clone 138258 3′. RC_R67996_at ze92g08.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA026417_at cDNA clone 366494 3′. H. sapiens partial cDNA sequence; clone c-33a10. RC_F11115_at yf21e07.s1 Homo sapiens cDNA clone 127524 3′. RC_R08871_at zr12e05.s1 Stratagene hNT neuron (#937233) Homo sapiens RC_AA224324_at cDNA clone 648608 3′. zt50c01.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA399226_at clone 725760 3′. yi25f09.r1 Homo sapiens cDNA clone 140297 5′ similar to R66920_at contains Alu repetitive element;. zx81a05.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA464240_s_at clone 810128 3′. zv08g07.r1 Soares NhHMPu S1 Homo sapiens cDNA clone AA436536_at 753084 5′. yz34f07.s1 Homo sapiens cDNA clone 284965 3′. RC_N71875_at zk10b03.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA029288_at cDNA clone 470093 3′ similar to PIR: H45193 H45193 zinc finger protein ZNF65;. yl63h11.r1 Homo sapiens cDNA clone 162981 5′ similar to H27242_at SP: GCN5_YEAST Q03330 TRANSCRIPTIONAL ACTIVATOR;. Human cytochrome P450 PCN3 gene, complete cds J04813_s_at aa32h08.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA465093_at IMAGE: 815007 3′. zs91c05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA282791_at IMAGE: 704840 3′. zx83f04.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA464180_at clone 810367 3′ similar to gb: M38188 OVARIAN GRANULOSA CELL 13.0 KD PROTEIN HGR74 (HUMAN);. zo03d03.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA149987_at clone 566597 3′. zr82h09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA256680_at 682241 3′. zl50c12.r1 Soares pregnant uterus NbHPU Homo sapiens AA147510_s_at cDNA clone 505366 5′. yi80c10.r1 Homo sapiens cDNA clone 145554 5′. R78119_at H. sapiens partial cDNA sequence; clone c-0ac03. RC_Z38407_s_at zs58f12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA287107_s_at IMAGE: 701711 3′. zs57e07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA287042_at IMAGE: 701604 3′. ab35g04.r1 Stratagene HeLa cell s3 937216 Homo sapiens AA489299_at cDNA clone 842838 5′. aa63f03.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone AA504744_at IMAGE: 825629 5′. zu47g07.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA402622_at clone 741180 3′. zw55e10.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA436628_at cDNA clone 773994 3′. zt02a10.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA282138_at IMAGE: 711930 3′. zk75a04.r1 Soares pregnant uterus NbHPU Homo sapiens AA045870_at cDNA clone 488622 5′. zv94b04.r1 Soares NhHMPu S1 Homo sapiens cDNA clone AA418098_at 767407 5′. zr65f06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA242799_at 668291 3′ similar to SW: SPO8_YEAST P41833 TRANSCRIPTIONAL REGULATOR SPO8.[1];. af12f04.s1 Soares testis NHT Homo sapiens cDNA clone RC_AA609210_at 1031455 3′. zo13e11.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA133469_at clone 586796 3′. yh25b11.r1 Homo sapiens cDNA clone 130749 5′. R22139_at EST176117 Colon carcinoma (Caco-2) cell line II Homo sapiens AA305116_at cDNA 5′ end. zk05c12.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA027954_at cDNA clone 469654 3′. zk29e11.r1 Soares pregnant uterus NbHPU Homo sapiens AA036900_at cDNA clone 471980 5′. ze92d07.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA026397_at cDNA clone 366445 3′. Human fetal brain cDNA 3′-end GEN-079C04. RC_D59981_s_at zs47c07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA284143_at IMAGE: 700620 3′. zb08f12.r1 Soares fetal lung NbHL19W Homo sapiens cDNA W16686_at clone 301487 5′. yw28c11.r1 Homo sapiens cDNA clone 253556 5′. H89575_s_at zs07g11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA251003_at IMAGE: 684548 3′. zs84h09.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA279408_at IMAGE: 704225 3′. zt07g10.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA281760_at IMAGE: 712482 3′ similar to TR: G808826 G808826 HYPOTHETICAL 25.7 KD PROTEIN.;. Human mRNA for KIAA0383 gene, partial cds. AB002381_at zx89d08.r1 Soares ovary tumor NbHOT Homo sapiens cDNA AA459542_s_at clone 810927 5′ similar to TR: G608025 G608025 ANKYRING.;. zl07b12.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA115559_at cDNA clone 491615 3′. ye36a05.r1 Homo sapiens cDNA clone 119792 5′. T94506_at Human fetal brain cDNA 5′-end GEN-404F02. D55869_s_at Homo sapiens (clone pZ50-19) cleavage stimulation factor L02547_at 50 kDa subunit, complete cds Human syntaxin 7 mRNA, complete cds. U77942_at zw76e03.r1 Soares testis NHT Homo sapiens cDNA clone AA431505_at 782140 5′. zr38c08.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA194045_at 665678 3′. ze78f05.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA025104_at cDNA clone 365121 3′. zr65e09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA242822_at 668296 3′. zs50f04.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA287388_at IMAGE: 700927 3′. hfe0045.seq.F Human fetal heart, Lambda ZAP Express Homo AA247679_at sapiens cDNA 5′. ab41e08.s1 Stratagene HeLa cell s3 937216 Homo sapiens RC_AA489383_at cDNA clone 843398 3′. zu81a08.s1 Soares testis NHT Homo sapiens cDNA clone RC_AA621188_at 744374 3′. ab35a01.s1 Stratagene HeLa cell s3 937216 Homo sapiens RC_AA486182_at cDNA clone 842760 3′. zv64h01.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA393876_s_at cDNA clone 758467 3′. zi06h12.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens RC_AA034189_at cDNA clone 430055 3′. ze79b09.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA024866_at cDNA clone 365177 3′. zx05h06.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA450373_at cDNA clone 785627 3′. yz78d07.r1 Homo sapiens cDNA clone 289165 5′. N78483_at zs94d07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA281245_at IMAGE: 705133 3′. zc45b12.r1 Soares senescent fibroblasts NbHSF Homo sapiens W52431_at cDNA clone 325247 5′ similar to SW: WDNM_RAT P14730 WDNM1 PROTEIN. [2] PIR: S07807;. zw84f01.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA446597_at cDNA clone 783673 3′. zr81h11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA256996_at 682149 3′. H. sapiens gene for cytokeratin 20 X73501_at zt20g02.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA287131_at clone 713714 3′ similar to TR: E124071 E124071 NAD+- ISOCITRATE DEHYDROGENASE;.

In a preferred embodiment genes from the first gene group is preferably selected individually from genes comprising a sequence as identified below by EST

RC_N23319_at yx78e10.s1 Homo sapiens cDNA clone 267882 3′. RC_R43812_at yg21a08.s1 Homo sapiens cDNA clone 32940 3′. RC_W37778_f_at zc13b12.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322175 3′ similar to contains LTR2.t3 LTR2 repetitive element;. RC_AA001045_at ze47b04.s1 Soares retina N2b4HR Homo sapiens cDNA clone 362095 3′. RC_AA086005_at zl84c04.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 511302 3′. RC_AA191524_at zp88f04.s1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 627295 3′. RC_AA219653_at zr05e02.s1 Stratagene NT2 neuronal precursor 937230 Homo sapiens cDNA clone 650618 3′. RC_AA252765_at zs27d03.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 686405 3′. RC_AA293300_s_(—) zt28d03.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 714437 3′. RC_AA405832_at zu57g11.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 742148 3′ similar to TR: G780241 G780241 AU-BINDING PROTEIN/ENOYL-COA HYDRATASE.;. X73501_at H. sapiens gene for cytokeratin 20 AA046768_at zk72d02.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 488355 5′. AA314457_at EST186294 Colon carcinoma (HCC) cell line II Homo sapiens cDNA 5′ end. AA324825_at EST27743 Cerebellum II Homo sapiens cDNA 5′ end.

In another embodiment a gene from the first gene group is selected individually from genes comprising a sequence as identified below by EST

Human mRNA for KIAA0372 gene, complete cds. AB002370_at Homo sapiens purinergic receptor P2Y5 mRNA, complete AF000546_at cds. yo70c03.r1 Homo sapiens cDNA clone 183268 5′. H43922_at yp17b05.r1 Homo sapiens cDNA clone 187665 5′ similar H44269_at to contains Alu repetitive element;. yw23e08.r1 Homo sapiens cDNA clone 253094 5′. H88706_s_at Homo sapiens epoxide hydrolase (EPHX) gene, complete L25880_s_at cds yw36d01.r1 Homo sapiens cDNA clone 254305 5′. N81162_at H. sapiens partial cDNA sequence; clone c-3ec07. RC_F10381_s_at EST00018 HE6W Homo sapiens cDNA clone RC_H54558_at HE6WCR108 3′. yr20g08.s1 Homo sapiens cDNA clone 205886 3′ similar RC_H58692_s_at to SP: FTDH_RAT P28037 FORMYLTETRAHYDROFOLATE DEHYDROGENASE;. yx28d06.s1 Homo sapiens cDNA clone 263051 3′. RC_N20047_at yv28e04.s1 Homo sapiens cDNA clone 244062 3′. RC_N38810_at yg51h01.s1 Homo sapiens cDNA clone 36305 3′. RC_R46497_at yj76a08.s1 Homo sapiens cDNA clone 154646 3′. RC_R55001_at EST10130 Homo sapiens cDNA 3′ end similar to None. RC_T29986_s_at EST12901 Homo sapiens cDNA 3′ end similar to None. RC_T30214_at ya01c07.s2 Homo sapiens cDNA clone 60204 3′. RC_T40438_at zc37f06.s1 Soares senescent fibroblasts NbHSF Homo RC_W51910_at sapiens cDNA clone 324515 3′. zd71f09.s1 Soares fetal heart NbHH19W Homo sapiens RC_W73949_at cDNA clone 346121 3′. zh55a02.s1 Soares fetal liver spleen 1NFLS S1 Homo RC_W86375_s_at sapiens cDNA clone 415946 3′. H. sapiens partial cDNA sequence; clone c-05e04. RC_Z38289_at H. sapiens partial cDNA sequence; clone c-0qb04. RC_Z38807_s_at H. sapiens partial cDNA sequence; clone c-1ed10. RC_Z39599_at ze74h03.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA025351_at cDNA clone 364757 3′ similar to contains OFR.t1 OFR repetitive element;. zl01f04.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA136474_at cDNA clone 491071 3′. zk99b02.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA136611_at cDNA clone 490923 3′. zr48f07.s1 Soares NhHMPu S1 Homo sapiens cDNA RC_AA233375_at clone 666661 3′. zt36c05.s1 Soares ovary tumor NbHOT Homo sapiens RC_AA235621_s_at cDNA clone 724424 3′. zr72g02.s1 Soares NhHMPu S1 Homo sapiens cDNA RC_AA253331_at clone 668978 3′. zv64a10.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA393793_at cDNA clone 758394 3′. zv04a05.s1 Soares NhHMPu S1 Homo sapiens cDNA RC_AA419547_at clone 752624 3′. zu27d11.s1 Soares ovary tumor NbHOT Homo sapiens RC_AA421100_at cDNA clone 739221 3′. zw87f06.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA443277_at cDNA clone 783971 3′. zw84c05.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA446570_at cDNA clone 783656 3′. zw93c01.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA447123_at cDNA clone 784512 3′. zx06g09.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA449343_at cDNA clone 785728 3′. aa03a08.s1 Soares NhHMPu S1 Homo sapiens cDNA RC_AA456016_at clone 812150 3′. zv21f04.s1 Soares NhHMPu S1 Homo sapiens cDNA RC_AA479299_at clone 754303 3′. zv17d09.s1 Soares NhHMPu S1 Homo sapiens cDNA RC_AA479350_at clone 753905 3′ similar to contains element TAR1 TAR1 repetitive element;. Human leukemogenic homolog protein (MEIS1) mRNA, U85707_at complete cds Human multispanning membrane protein mRNA, complete U94831_at cds. /gb = U94831 /ntype = RNA 38c8 Human retina cDNA randomly primed sublibrary W27827_at Homo sapiens cDNA. zd85a12.r1 Soares fetal heart NbHH19W Homo sapiens W81301_at cDNA clone 347422 5′. H. sapiens mRNA for putative progesterone binding Y12711_at protein zm15c08.r1 Stratagene pancreas (#937208) Homo sapiens AA074407_at cDNA clone 525710 5′. yy1646.seq.F Fetal heart, Lambda ZAP Express Homo AA091017_at sapiens cDNA 5′. l7134.seq.F Fetal heart, Lambda ZAP Express Homo AA104023_at sapiens cDNA 5′. zo95d05.r1 Stratagene ovarian cancer (#937219) Homo AA171913_at sapiens cDNA clone 594633 5′. zr32h05.r1 Soares NhHMPu S1 Homo sapiens cDNA AA195678_at clone 665145 5′. zr55e05.r1 Soares NhHMPu S1 Homo sapiens cDNA AA227678_at clone 667328 5′. csg0306.seq.F Human fetal heart, Lambda ZAP Express AA247204_at Homo sapiens cDNA 5′. zv18b05.r1 Soares NhHMPu S1 Homo sapiens cDNA AA479995_at clone 753969 5′.

In one preferred embodiment a gene from the first gene group is selected individually from genes comprising a sequence as identified below by EST

AF000546_at Homo sapiens purinergic receptor P2Y5 mRNA, complete cds. L25880_s_at Homo sapiens epoxide hydrolase (EPHX) gene, complete cds RC_N20047_at yx28d06.s1 Homo sapiens cDNA clone 263051 3′. RC_W51910_at zc37f06.s1 Soares senescent fibroblasts NbHSF Homo sapiens cDNA clone 324515 3′. RC_W86375_s_at zh55a02.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 415946 3′. RC_Z38289_at H. sapiens partial cDNA sequence; clone c-05e04. RC_Z38807_s_at H. sapiens partial cDNA sequence; clone c-0qb04. RC_AA393793_at zv64a10.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 758394 3′. RC_AA446570_at zw84c05.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 783656 3′. RC_AA456016_at aa03a08.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 812150 3′. RC_AA479350_at zv17d09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 753905 3′ similar to contains element TAR1 TAR1 repetitive element;.

In yet another embodiment a gene from the first gene group is selected individually from genes comprising a sequence as identified below by EST

yl26e06.s1 Homo sapiens cDNA clone 159394 3′. RC_H14633_at yz74d02.s1 Homo sapiens cDNA clone 288771 3′. RC_N62506_at za74g10.s1 Homo sapiens cDNA clone 298338 3′. RC_N70481_at za57b06.s1 Homo sapiens cDNA clone 296627 3′. RC_N73988_at ya88g06.s1 Homo sapiens cDNA clone 68794 3′. RC_T53404_at H. sapiens partial cDNA sequence; clone c-01a09. RC_Z38149_at H. sapiens partial cDNA sequence; clone c-0rb11. RC_Z38849_at zc03h03.s1 Soares parathyroid tumor NbHPA Homo sapiens RC_AA037409_at cDNA clone 321269 3′. zn18b04.s1 Stratagene neuroepithelium NT2RAMI 937234 RC_AA084318_at Homo sapiens cDNA clone 547759 3′. zk94d04.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA126419_at cDNA clone 490471 3′. zm24d04.s1 Stratagene pancreas (#937208) Homo sapiens RC_AA128407_at cDNA clone 526567 3′. zp02e08.s1 Stratagene ovarian cancer (#937219) Homo sapiens RC_AA173430_at cDNA clone 595238 3′. zt58d03.s1 Soares testis NHT Homo sapiens cDNA clone RC_AA398104_at 726533 3′. zt50e07.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA399414_at clone 725796 3′. zw72f05.s1 Soares testis NHT Homo sapiens cDNA clone RC_AA431479_at 781761 3′. zv08e05.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA436471_at 753056 3′. zx05e10.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA449455_at cDNA clone 785610 3′ similar to contains Alu repetitive element;. zx88d07.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA458899_at clone 810829 3′. zx98g09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA463630_s_at 811840 3′. aa54d11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA489009_at IMAGE: 824757 3′. zc11f08.r1 Soares parathyroid tumor NbHPA Homo sapiens W37319_at cDNA clone 322023 5′.

In a preferred embodiment a gene from the first gene group is selected individually from genes comprising a sequence as identified below by EST

N75611_s_at yw37b04.r1 Homo sapiens cDNA clone 254383 5′. RC_H20769_at yn64a06.s1 Homo sapiens cDNA clone 173170 3′. RC_R54822_at yg87f06.s1 Homo sapiens cDNA clone 40364 3′. RC_AA058357_s_(—) zl67e01.s1 Stratagene colon (#937204) Homo sapiens cDNA at clone 509688 3′ similar to TR: G189087 G189087 NONSPECIFIC CROSSREACTING ANTIGEN.;. RC_AA086487_at zn53a05.s1 Stratagene muscle 937209 Homo sapiens cDNA clone 561872 3′ similar to contains Alu repetitive element;. RC_AA456289_at aa13e06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 813154 3′. RC_AA609539_at af14g11.s1 Soares testis NHT Homo sapiens cDNA clone 1031684 3′.

In another embodiment a gene from the first gene group is selected individually from genes comprising a sequence as identified below by EST

N24990_s_at yx16e10.r1 Homo sapiens cDNA clone 261930 5′. R11267_at yf41e08.r1 Homo sapiens cDNA clone 129446 5′ similar to SP: A46661 A46661 LEUKOTRIENE B4 OMEGA- HYDROXYLASE, P-450LTB OMEGA = CYTOCHROME P-450 SUPERFAMILY MEMBER-;. RC_H52937_at yq76e12.s1 Homo sapiens cDNA clone 201742 3′ similar to gb: J02982 GLYCOPHORIN B PRECURSOR (HUMAN);. RC_H69547_at yr89e02.s1 Homo sapiens cDNA clone 212474 3′. RC_H70047_at yu73c12.s1 Homo sapiens cDNA clone 239446 3′. RC_N24879_at yx99c11.s1 Homo sapiens cDNA clone 269876 3′. RC_N66312_at yz38a06.s1 Homo sapiens cDNA clone 285298 3′. RC_R22189_at yh26a02.s1 Homo sapiens cDNA clone 130826 3′. RC_R45582_at yg44f05.s1 Homo sapiens cDNA clone 35270 3′. RC_R53457_at yg83e10.s1 Homo sapiens cDNA clone 39835 3′. RC_R70903_at yi49g10.s1 Homo sapiens cDNA clone 142626 3′. RC_AA054321_s_(—) zl68c01.s1 Stratagene colon (#937204) Homo sapiens cDNA at clone 509760 3′. RC_AA099820_at zk87c05.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 489800 3′. RC_AA127238_at zl17g05.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 502232 3′. RC_AA147224_at zo64h02.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 591699 3′. RC_AA192765_at zq12e02.s1 Stratagene muscle 937209 Homo sapiens cDNA clone 629498 3′. RC_AA195718_at zr33d07.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 665197 3′. RC_AA232114_s_(—) zr28b08.s1 Stratagene NT2 neuronal precursor 937230 Homo at sapiens cDNA clone 664695 3′ similar to gb: L05779 SOLUBLE EPOXIDE HYDROLASE (HUMAN);. RC_AA281770_at zt07h12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 712487 3′. RC_AA430209_at zw59e03.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774364 3′ similar to TR: G1199667 G1199667 PROTEIN KINASE C-BINDING PROTEIN ENIGMA;. RC_AA452410_at zx31f03.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 788093 3′. RC_AA485115_at aa39g12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 815686 3′. AA099391_s_at zk85e12.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 489646 5′. AA131127_at zo16a05.r1 Stratagene colon (#937204) Homo sapiens cDNA clone 587024 5′ similar to SW: CATX_BOVIN P05689 CATHEPSIN;. AA173505_at zp02c06.r1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 595210 5′ similar to SW: QRI2_YEAST P43124 HYPOTHETICAL 46.1 KD PROTEIN IN PHO2-POL3 INTERGENIC REGION. [1];. AA291786_s_at zt39b07.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 724693 5′. AA402971_s_at zu53f10.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 741739 5′.

In yet another embodiment a gene from the first gene group is selected individually from genes comprising a sequence as identified below by EST

D84239_at Human mRNA for IgG Fc binding protein, complete cds RC_N54841_at yv73b09.s1 Soares fetal liver spleen 1NFLS Homo sapiens cDNA clone 248345 3′. RC_T53389_s_at ya88f04.s1 Homo sapiens cDNA clone 68767 3′. RC_T98227_at ye30d12.s1 Homo sapiens cDNA clone 119255 3′. RC_AA215379_at zr97c07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 683628 3′. RC_AA256485_at zr81e12.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 682126 3′. RC_AA290679_at zt19f03.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 713597 3′ similar to TR: E92665 E92665 AP56;. RC_AA425309_at zw46c01.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 773088 3′. RC_AA429655_at zw71d04.s1 Soares testis NHT Homo sapiens cDNA clone 781639 3′. RC_AA456981_at aa90h11.s1 Stratagene fetal retina 937202 Homo sapiens cDNA clone 838629 3′ similar to contains Alu repetitive element;. RC_AA461174_at zx70c04.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 796806 3′. W61377_at zd27g09.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 341920 5′. Second Gene Group

Genes that are up-regulated (or gained de novo) during the malignant progression of bladder cancer from normal tissue through Ta, T1, T2, T3 and T4 is also within the scope of the invention. These genes are potential oncogenes and may be those genes that create or enhance the malignant growth of the cells. The expression level of these genes may serve as predictive markers for the disease course and treatment response, as a high level may signal an aggressive disease course, and they may serve as targets for therapy, as blocking these genes by e.g. anti-sense therapy, or by biochemical means could inhibit, or slow the tumor growth. Such upregulated (or gained de novo) genes, oncogenes, may be classified according to the present invention as genes belonging to second genes group.

With respect to bladder tumors genes belonging to the second gene group at least one, such as at least two, for example at least three, such as at least four, such as at least five, such as more than six genes are being expressed and are preferably selected individually from genes comprising a sequence as identified below by EST

RC_AA116036_at zm79a11.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA clone 531836 3′. RC_AA101562_at zn76c11.s1 Stratagene NT2 neuronal precursor 937230 Homo sapiens cDNA clone 564116 3′ similar to contains Alu repetitive element;. RC_H20269_at yn53b04.s1 Homo sapiens cDNA clone 172111 3′. RC_Z40715_at H. sapiens partial cDNA sequence; clone c-2ea12. or a sequence as described below

AA402119_at zu55d04.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 741895 5′ similar to TR: G397579 G397579 LL5 MRNA. ;. RC_AA102581_at zn42d02.s1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 550083 3′. RC_H14089_at ym62c07.s1 Homo sapiens cDNA clone 163500 3′. RC_R46079_f_at yg49c02.s1 Homo sapiens cDNA clone 36133 3′. RC_R67918_at yi25g01.s1 Homo sapiens cDNA clone 140304 3′. RC_W15360_at zc17d10.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322579 3′ similar to PIR: S39983 S39983 eps8 protein - mouse;. AA082171_at zn42g07.r1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 550140 5′. AA425593_at zw48f02.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 773307 5′. F15201_at H. sapiens partial cDNA sequence. H15219_at ym30f02.r1 Homo sapiens cDNA clone 49693 5′. R60368_at yh04b02.r1 Homo sapiens cDNA clone 42052 5′. R86859_at ym86a02.r1 Homo sapiens cDNA clone 165770 5′. RC_AA045342_at zk59g01.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 487152 3′. RC_AA171985_at zo98g05.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 594968 3′. T63174_s_at yc04e08.r1 Homo sapiens cDNA clone 79718 5′ similar to contains Alu repetitive element;. U90268_at Human Krit1 mRNA, complete cds. X14787_at Human mRNA for thrombospondin RC_AA196991_s_(—) zq10a10.s1 Stratagene muscle 937209 Homo sapiens cDNA at clone 629274 3′ similar to TR: G1049074 G1049074 VASOPRESSIN- ACTIVATED CALCIUM-MOBILIZING PROTEIN. ;. RC_F02470_at H. sapiens partial cDNA sequence; clone c-10c01. RC_F08899_at H. sapiens partial cDNA sequence; clone c-2uc10. RC_H15259_at ym30c10.s1 Homo sapiens cDNA clone 49795 3′. RC_H52133_at yo44d04.s1 Homo sapiens cDNA clone 180775 3′. RC_R17059_at yf45a10.s2 Homo sapiens cDNA clone 129786 3′. RC_R45292_at yg46b01.s1 Homo sapiens cDNA clone 35626 3′. or a sequence as described below

C01360_at HUMGS0008341, Human Gene Signature, 3′-directed cDNA sequence. D80002_at Human mRNA for KIAA0180 gene, partial cds RC_AA149586_at zl39e03.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504316 3′. RC_H68772_at yr83f01.s1 Homo sapiens cDNA clone 211897 3′. RC_N30806_at yw65f02.s1 Homo sapiens cDNA clone 257115 3′. RC_N63143_at yz37c12.s1 Homo sapiens cDNA clone 285238 3′. RC_R33146_at yh81f02.s1 Homo sapiens cDNA clone 136155 3′ similar to contains Alu repetitive element;. RC_R46206_at yj53d08.s1 Homo sapiens cDNA clone 152463 3′. RC_R49731_s_at yg71e10.s1 Homo sapiens cDNA clone 38554 3′. AA043223_at zk55g12.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486790 5′. AB002346_at Human mRNA for KIAA0348 gene, complete cds. D81608_at Human fetal brain cDNA 5′-end GEN-177B09. M83670_s_at Human carbonic anhydrase IV mRNA, complete cds N28843_at yx59d10.r1 Homo sapiens cDNA clone 266035 5′. RC_AA149044_at zl45d09.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504881 3′. RC_AA258130_at zs35f03.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 687197 3′. RC_AA281743_r_(—) zt06h05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone at IMAGE: 712377 3′. RC_AA406338_at zv10f06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 753251 3′. RC_AA424524_at zv90g02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 767090 3′. RC_AA435840_at zt80b08.s1 Soares testis NHT Homo sapiens cDNA clone 728631 3′. RC_AA027823_at zk05c04.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 469638 3′. RC_AA084138_at zn17a03.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 547660 3′. RC_AA135406_at zo28e08.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 588230 3′. RC_AA148923_at zl27g11.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 503204 3′. RC_H98653_at yx12h06.s1 Homo sapiens cDNA clone 261563 3′. RC_N30077_at yw81g11.s1 Homo sapiens cDNA clone 258692 3′. RC_R40166_at yf70a09.s1 Homo sapiens cDNA clone 27448 3′. RC_T90374_at yd43e03.s1 Homo sapiens cDNA clone 111004 3′ similar to SP: POL2_MOUSE P11369 RETROVIRUS-RELATED POL POLYPROTEIN;. RC_Z38182_at H. sapiens partial cDNA sequence; clone c-02a08. or a sequence as described below

RC_AA054726_at Zk68e06.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 488002 3′. RC_AA206042_at Zq77f02.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA clone 647643 3′ similar to contains element MSR1 repetitive element;. RC_R98735_at Yr31g12.s1 Homo sapiens cDNA clone 206950 3′. AA115572_s_at Zl05d11.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491445 5′ similar to TR: G895845 G895845 PUTATIVE P64 CLCP PROTEIN. ;. AA430979_at PMY0789 KG1a Lambda Zap Express cDNA Library Homo sapiens cDNA 5′. AA489287_at ab36e04.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842910 5′. D82226_s_at similar to TAT-binding protein-2. H49499_s_at yq20g10.r1 Soares fetal liver spleen 1NFLS Homo sapiens cDNA clone 274386 5′. M11844_at Human prealbumin gene, complete cds. RC_AA026388_at ze92c03.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366436 3′. RC_AA044601_at zk55d05.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486729 3′. RC_AA182030_at zp57a03.s1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 624268 3′. RC_AA233451_at zr30b02.s1 Stratagene NT2 neuronal precursor 937230 Homo sapiens cDNA clone 664875 3′. RC_AA236493_at zr75c10.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 669234 3′. RC_AA401098_f_(—) zu50g01.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 741456 3′ similar to contains Alu repetitive element; contains element THR repetitive element;. RC_AA441818_at zw62f01.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774649 3′. RC_AA478109_at zt89d04.s1 Soares testis NHT Homo sapiens cDNA clone 729511 3′. RC_AA481430_at zv06g11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 752900 3′. RC_AA488878_at aa55f02.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 824859 3′. RC_AA599032_at ae41h03.s1 Gessler Wilms tumor Homo sapiens cDNA clone 898421 3′. S73288_at small proline-rich protein SPRK [human, odontogenic keratocysts, mRNA Partial, 317 nt]. U87459_at Human autoimmunogenic cancer/testis antigen NY-ESO-1 mRNA, complete cds U88047_at Human DNA binding protein homolog (DRX) mRNA, partial cds RC_AA063574_at ze25f03.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 360029 3′ similar to gb: X52104 P68 PROTEIN (HUMAN);. RC_AA132524_at zo20c04.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587430 3′ similar to contains Alu repetitive element;. RC_F09317_at H. sapiens partial cDNA sequence; clone c-2zh11. RC_H12863_at yj14b12.s1 Homo sapiens cDNA clone 148703 3′. RC_N33927_s_at yv25e09.s1 Homo sapiens cDNA clone 243784 3′. RC_R08189_at yf18f03.s1 Homo sapiens cDNA clone 127229 3′. RC_R39191_s_at yc89c12.s1 Homo sapiens cDNA clone 23345 3′. RC_T82323_at AS322 Homo sapiens cDNA clone AS322 3′. RC_T90746_at yd41f10.s1 Homo sapiens cDNA clone 110827 3′. RC_Z39338_at H. sapiens partial cDNA sequence; clone c-17f11. or a sequence as described below

AA011479_at zi01b10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429499 5′. AA314779_at EST186601 Colon carcinoma (HCC) cell line II Homo sapiens cDNA 5′ end, RC_AA084640_at zn20d05.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 547977 3′. RC_AA121534_at zk89d11.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 490005 3′ similar to gb: X79535 TUBULIN BETA-2 CHAIN (HUMAN);. RC_AA131047_s_(—) zo16f05.s1 Stratagene colon (#937204) Homo sapiens cDNA at clone 587073 3′. RC_AA461549_at zx62b09.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 796025 3′. RC_AA491465_at ab04a05.s1 Stratagene fetal retina 937202 Homo sapiens cDNA clone 839792 3′. RC_AA496936_at ae32d03.s1 Gessler Wilms tumor Homo sapiens cDNA clone 897509 3′. RC_AA598689_at ae49a08.s1 Stratagene lung carcinoma 937218 Homo sapiens cDNA clone 950198 3′. W26392_at 30g3 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA, RC_AA004887_at zh90g01.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 428592 3′. RC_AA135153_at zo24g02.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587858 3′. RC_AA197311_s_(—) zq50e09.s1 Stratagene neuroepithelium (#937231) Homo sapiens at cDNA clone 645064 3′ similar to gb: M24283 INTERCELLULAR ADHESION MOLECULE-1 PRECURSOR (HUMAN);. RC_H80622_at yu77b06.s1 Homo sapiens cDNA clone 239795 3′. RC_N64436_at za33a09.s1 Homo sapiens cDNA clone 294328 3′. RC_N67583_at yz42c02.s1 Homo sapiens cDNA clone 285698 3′. RC_R38678_at yc89d05.s1 Homo sapiens cDNA clone 23443 3′. RC_R56066_s_at yg91d08.s1 Homo sapiens cDNA clone 40992 3′. RC_R59292_at yh16a10.s1 Homo sapiens cDNA clone 37689 3′. RC_T24099_at seq2287 Homo sapiens cDNA clone Cot250Ft-b4HB3MA-8 3′. AA150364_at zl07b03.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491597 5′. AA174185_at PTH207 HTCDL1 Homo sapiens cDNA 5′/3′. AA452353_i_at zx15d05.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 786537 5′. AB002316_at Human mRNA for KIAA0318 gene, partial cds, H86858_at ys72d05.r1 Homo sapiens cDNA clone 220329 5′. M93119_s_at Human zinc-finger DNA-binding motifs (IA-1) mRNA, complete cds R72037_at yj86c09.r1 Homo sapiens cDNA clone 155632 5′. RC_AA004274_at zh97f02.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429243 3′ similar to contains element MER22 repetitive element;. RC_AA004415_at zh89b04.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 428431 3′. RC_AA007160_at 13cDNA30A-3, seq Soares infant brain 1NIB Homo sapiens cDNA clone HY18-3 3′. RC_AA053660_at zl74e07.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 510372 3′ similar to contains Alu repetitive element;. RC_AA252603_at zs14a11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 685148 3′. RC_AA411944_at zu03h01.s1 Soares testis NHT Homo sapiens cDNA clone 730801 3′. RC_AA412700_at zu12g03.s1 Soares testis NHT Homo sapiens cDNA clone 731668 3′. RC_AA430032_at zw65f05.s1 Soares testis NHT Homo sapiens cDNA clone 781089 3′. RC_AA430368_at zw20f06.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 769859 3′. RC_AA434113_at zw24b11.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 770205 3′ similar to contains element TAR1 repetitive element;. RC_AA441791_at zw62c02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774626 3′. RC_AA449419_at zx05b03.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 785549 3′. RC_AA449914_at zx37g02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 788690 3′. RC_D59847_at Human fetal brain cDNA 3′-end GEN-070G07, T95813_f_at ye45f10.r1 Homo sapiens cDNA clone 120715 5′ similar to gb: V00493_rna1 HEMOGLOBIN ALPHA CHAIN (HUMAN);. W80846_at zd83f05.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 347265 5′ similar to SW: SYB2_XENLA P47193 SYNAPTOBREVIN 2;. RC_AA031360_s_(—) zk16f07.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA at clone 470725 3′. RC_AA063624_at ze87h05.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366009 3′ similar to TR: G300372 G300372 CELL GROWTH REGULATING NUCLEOLAR PROTEIN,;; RC_AA076238_at zm19e04.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 526110 3′ similar to contains Alu repetitive element;. RC_AA076350_at zm91a02.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 545258 3′. RC_AA101983_at zk87c02.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 489794 3′. RC_AA151245_at zl40f12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504431 3′. RC_AA164252_f_(—) zq46f06.s1 Stratagene hNT neuron (#937233) Homo sapiens at cDNA clone 632771 3′. RC_AA167006_at zo86b08.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 593751 3′. RC_AA206225_at zq56g08.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA clone 645662 3′. RC_D62834_at Human aorta cDNA 3′-end GEN-330D04, RC_D80981_at Human fetal brain cDNA 3′-end GEN-121E12, RC_H16772_at ym34g02.s1 Homo sapiens cDNA clone 50227 3′. RC_N62522_at yz74f08.s1 Homo sapiens cDNA clone 288807 3′. RC_N68222_at yz56e12.s1 Homo sapiens cDNA clone 287086 3′. RC_T10316_s_at seq1014 Homo sapiens cDNA clone b4HB3MA-COT8-HAP- Ft266 3′. RC_W37382_at zc12c07.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322092 3′. RC_W60582_at zd25e10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 341706 3′ similar to gb: M38188 OVARIAN GRANULOSA CELL 13.0 KD PROTEIN HGR74 (HUMAN);. RC_W84768_at zh53d03.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 415781 3′ similar to contains L1, b1 L1 repetitive element;. or a sequence as described below

RC_AA176164_i_(—) zp23h11.s1 Stratagene neuroepithelium (#937231) Homo at sapiens cDNA clone 610341 3′. W52431_at zc45b12.r1 Soares senescent fibroblasts NbHSF Homo sapiens cDNA clone 325247 5′ similar to SW: WDNM_RAT P14730 WDNM1 PROTEIN, [2] PIR: S07807;. RC_AA019641_at ze62g03.s1 Soares retina N2b4HR Homo sapiens cDNA clone 363604 3′ similar to contains element L1 repetitive element;. RC_H13696_at yj09e04.s1 Homo sapiens cDNA clone 148254 3′. RC_N22404_at yw37h03.s1 Homo sapiens cDNA clone 254453 3′. RC_R07501_at ye97f06.s1 Homo sapiens cDNA clone 125699 3′. C14412_s_at Human fetal brain cDNA 5′-end GEN-055A09, RC_AA236455_s_(—) zr75g02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone at 669266 3′. RC_AA417030_at zu04e07.s1 Soares testis NHT Homo sapiens cDNA clone 730884 3′. RC_F10945_at H. sapiens partial cDNA sequence; clone c-3mb07, RC_N29319_at yw84a11.s1 Homo sapiens cDNA clone 258908 3′. RC_N68038_f_at yz53a12.s1 Homo sapiens cDNA clone 286750 3′. or a sequence as described below

RC_AA417030_at zu04e07.s1 Soares testis NHT Homo sapiens cDNA clone 730884 3′. RC_AA608545_at ae53d05.s1 Stratagene lung carcinoma 937218 Homo sapiens cDNA clone 950601 3′. RC_H09261_at y198c12.s1 Homo sapiens cDNA clone 46410 3′ similar to contains Alu repetitive element; contains MSR1 repetitive element;. RC_N68871_at za23h07.s1 Homo sapiens cDNA clone 293437 3′ similar to contains Alu repetitive element;. AA129196_at zn29d08.r1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 548847 5′ similar to SW: NU1M_MOUSE P03888 NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 1;. RC_AA620553_(—) ae58g12.s1 Stratagene lung carcinoma 937218 Homo sapiens s_at cDNA clone 951142 3′. RC_F10779_at H. sapiens partial cDNA sequence; clone c-3jg08. RC_F10945_at H. sapiens partial cDNA sequence; clone c-3mb07. RC_H65650_at yr72d10.s1 Homo sapiens cDNA clone 210835 3′. RC_N68038_f_at yz53a12.s1 Homo sapiens cDNA clone 286750 3′. or a sequence as described below

RC_AA417030_at zu04e07.s1 Soares testis NHT Homo sapiens cDNA clone 730884 3′. RC_AA608545_at ae53d05.s1 Stratagene lung carcinoma 937218 Homo sapiens cDNA clone 950601 3′. RC_F10945_at H. sapiens partial cDNA sequence; clone c-3mb07. RC_N68038_f_at yz53a12.s1 Homo sapiens cDNA clone 286750 3′.

In one embodiment the genes belonging to the second gene group are preferably selected individually from genes comprising sequences as identified below by EST

AB000221_at Homo sapiens mRNA for CC chemokine, complete cds. RC_D60296_at Human fetal brain cDNA 3′-end GEN-097D06. RC_D60813_at Human fetal brain cDNA 3′-end GEN-132E11. RC_R49708_s_at Yg71a11.s1 Homo sapiens cDNA clone 38542 3′. RC_Z38182_at H. sapiens partial cDNA sequence; clone c-02a08. RC_AA456821_at Aa38e07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 815556 3′. RC_AA608545_at ae53d05.s1 Stratagene lung carcinoma 937218 Homo sapiens cDNA clone 950601 3′. RC_AA620553_s_(—) ae58g12.s1 Stratagene lung carcinoma 937218 Homo sapiens at cDNA clone 951142 3′. AA095119_at cp3087.seq.F Fetal heart, Lambda ZAP Express Homo sapiens cDNA 5′.

In another embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST

M63180_at Human threonyl-tRNA synthetase mRNA, complete cds N89563_s_at HFBEST-40 Human fetal brain QBoqin2 Homo sapiens cDNA. RC_D80198_at Human fetal brain cDNA 3′-end GEN-045C11. RC_F01986_f_at H. sapiens partial cDNA sequence; clone c-0kf11. RC_H18997_at yn51g07.s1 Homo sapiens cDNA clone 171996 3′. RC_AA101562_at zn76c11.s1 Stratagene NT2 neuronal precursor 937230 Homo sapiens cDNA clone 564116 3′ similar to contains Alu repetitive element;.

In yet another embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST.

RC_H20269_at yn53b04.s1 Homo sapiens cDNA clone 172111 3′. RC_Z40715_at H. sapiens partial cDNA sequence; clone c-2ea12. RC_AA116036_at zm79a11.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA clone 531836 3′. RC_AA133250_at zn92a08.s1 Stratagene lung carcinoma 937218 Homo sapiens cDNA clone 565622 3′.

In a further embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST.

RC_R00083_at ye73c08.s1 Homo sapiens cDNA clone 123374 3′. RC_R71391_at yj80e01.s1 Homo sapiens cDNA clone 155064 3′. RC_T23991_at seq2147 Homo sapiens cDNA clone NHB3MK-9 3′. RC_T79196_at yd70f06.s1 Homo sapiens cDNA clone 113603 3′ similar to contains Alu repetitive element;. RC_AA130596_at zo26a09.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587992 3′. RC_AA459310_r_(—) zx89d06.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 810923 3′. RC_AA490965_at aa48f12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 824207 3′. U88047_at Human DNA binding protein homolog (DRX) mRNA, partial cds X56807_at Human DSC2 mRNA for desmocollins type 2a and 2b AA011479_at zi01b10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429499 5′. AA296821_at EST112387 Aorta endothelial cells Homo sapiens cDNA 5′ end.

In a preferred embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST.

RC_AA054726_at zk68e06.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 488002 3′. RC_AA206042_at zq77f02.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA clone 647643 3′ similar to contains element MSR1 repetitive element;. RC_R98735_at yr31g12.s1 Homo sapiens cDNA clone 206950 3′. AA115572_s_at zl05d11.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491445 5′ similar to TR: G895845 G895845 PUTATIVE P64 CLCP PROTEIN, ;. AA430979_at PMY0789 KG1a Lambda Zap Express cDNA Library Homo sapiens cDNA 5′. AA489287_at ab36e04.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842910 5′. D82226_s_at similar to TAT-binding protein-2. H49499_s_at yq20g10.r1 Soares fetal liver spleen 1NFLS Homo sapiens cDNA clone 274386 5′. M11844_at Human prealbumin gene, complete cds. RC_AA026388_at ze92c03.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366436 3′. RC_AA044601_at zk55d05.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486729 3′. RC_AA182030_at zp57a03.s1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 624268 3′. RC_AA233451_at zr30b02.s1 Stratagene NT2 neuronal precursor 937230 Homo sapiens cDNA clone 664875 3′. RC_AA236493_at zr75c10.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 669234 3′. RC_AA401098_f_(—) zu50g01.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 741456 3′ similar to contains Alu repetitive element; contains element THR repetitive element;. RC_AA441818_at zw62f01.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774649 3′. RC_AA478109_at zt89d04.s1 Soares testis NHT Homo sapiens cDNA clone 729511 3′. RC_AA481430_at zv06g11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 752900 3′. RC_AA488878_at aa55f02.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 824859 3′. RC_AA599032_at ae41h03.s1 Gessler Wilms tumor Homo sapiens cDNA clone 898421 3′. S73288_at small proline-rich protein SPRK [human, odontogenic keratocysts. mRNA Partial, 317 nt]. U87459_at Human autoimmunogenic cancer/testis antigen NY-ESO-1 mRNA, complete cds U88047_at Human DNA binding protein homolog (DRX) mRNA, partial cds RC_AA063574_at ze25f03.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 360029 3′ similar to gb: X52104 P68 PROTEIN (HUMAN);. RC_AA132524_at zo20c04.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587430 3′ similar to contains Alu repetitive element;. RC_F09317_at H. sapiens partial cDNA sequence; clone c-2zh11. RC_H12863_at yj14b12.s1 Homo sapiens cDNA clone 148703 3′. RC_N33927_s_at yv25e09.s1 Homo sapiens cDNA clone 243784 3′. RC_R08189_at yf18f03.s1 Homo sapiens cDNA clone 127229 3′. RC_R39191_s_at yc89c12.s1 Homo sapiens cDNA clone 23345 3′. RC_T82323_at AS322 Homo sapiens cDNA clone AS322 3′. RC_T90746_at yd41f10.s1 Homo sapiens cDNA clone 110827 3′. RC_Z39338_at H. sapiens partial cDNA sequence; clone c-17f11. AA011479_at zi01b10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429499 5′. AA314779_at EST186601 Colon carcinoma (HCC) cell line II Homo sapiens cDNA 5′ end. RC_AA084640_at zn20d05.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 547977 3′. RC_AA121534_at zk89d11.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 490005 3′ similar to gb: X79535 TUBULIN BETA-2 CHAIN (HUMAN);. RC_AA131047_s_(—) zo16f05.s1 Stratagene colon (#937204) Homo sapiens cDNA at clone 587073 3′. RC_AA461549_at zx62b09.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 796025 3′. RC_AA491465_at ab04a05.s1 Stratagene fetal retina 937202 Homo sapiens cDNA clone 839792 3′. RC_AA496936_at ae32d03.s1 Gessler Wilms tumor Homo sapiens cDNA clone 897509 3′. RC_AA598689_at ae49a08.s1 Stratagene lung carcinoma 937218 Homo sapiens cDNA clone 950198 3′. W26392_at 30g3 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA. RC_AA004887_at zh90g01.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 428592 3′. RC_AA135153_at zo24g02.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587858 3′. RC_AA197311_s_(—) zq50e09.s1 Stratagene neuroepithelium (#937231) Homo sapiens at cDNA clone 645064 3′ similar to gb: M24283 INTERCELLULAR ADHESION MOLECULE-1 PRECURSOR (HUMAN);. RC_H80622_at yu77b06.s1 Homo sapiens cDNA clone 239795 3′. RC_N64436_at za33a09.s1 Homo sapiens cDNA clone 294328 3′. RC_N67583_at yz42c02.s1 Homo sapiens cDNA clone 285698 3′. RC_R38678_at yc89d05.s1 Homo sapiens cDNA clone 23443 3′. RC_R56066_s_at yg91d08.s1 Homo sapiens cDNA clone 40992 3′. RC_R59292_at yh16a10.s1 Homo sapiens cDNA clone 37689 3′. RC_T24099_at seq2287 Homo sapiens cDNA clone Cot250Ft-b4HB3MA-8 3′. AA150364_at zl07b03.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491597 5′. AA174185_at PTH207 HTCDL1 Homo sapiens cDNA 5′/3′. AA452353_i_at zx15d05.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 786537 5′. AB002316_at Human mRNA for KIAA0318 gene, partial cds. H86858_at ys72d05.r1 Homo sapiens cDNA clone 220329 5′. M93119_s_at Human zinc-finger DNA-binding motifs (IA-1) mRNA, complete cds R72037_at yj86c09.r1 Homo sapiens cDNA clone 155632 5′. RC_AA004274_at zh97f02.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429243 3′ similar to contains element MER22 repetitive element;. RC_AA004415_at zh89b04.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 428431 3′. RC_AA007160_at 13cDNA30A-3, seq Soares infant brain 1NIB Homo sapiens cDNA clone HY18-3 3′. RC_AA053660_at zl74e07.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 510372 3′ similar to contains Alu repetitive element;. RC_AA252603_at zs14a11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 685148 3′. RC_AA411944_at zu03h01.s1 Soares testis NHT Homo sapiens cDNA clone 730801 3′. RC_AA412700_at zu12g03.s1 Soares testis NHT Homo sapiens cDNA clone 731668 3′. RC_AA430032_at zw65f05.s1 Soares testis NHT Homo sapiens cDNA clone 781089 3′. RC_AA430368_at zw20f06.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 769859 3′. RC_AA434113_at zw24b11.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 770205 3′ similar to contains element TAR1 repetitive element;. RC_AA441791_at zw62c02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774626 3′. RC_AA449419_at zx05b03.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 785549 3′. RC_AA449914_at zx37g02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 788690 3′. RC_D59847_at Human fetal brain cDNA 3′-end GEN-070G07. T95813_f_at ye45f10.r1 Homo sapiens cDNA clone 120715 5′ similar to gb: V00493_rna1 HEMOGLOBIN ALPHA CHAIN (HUMAN);. W80846_at zd83f05.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 347265 5′ similar to SW: SYB2_XENLA P47193 SYNAPTOBREVIN 2;. RC_AA031360_s_(—) zk16f07.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA at clone 470725 3′. RC_AA063624_at ze87h05.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366009 3′ similar to TR: G300372 G300372 CELL GROWTH REGULATING NUCLEOLAR PROTEIN,;. RC_AA076238_at zm19e04.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 526110 3′ similar to contains Alu repetitive element;. RC_AA076350_at zm91a02.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 545258 3′. RC_AA101983_at zk87c02.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 489794 3′. RC_AA151245_at zl40f12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504431 3′. RC_AA164252_f_(—) zq46f06.s1 Stratagene hNT neuron (#937233) Homo sapiens at cDNA clone 632771 3′. RC_AA167006_at zo86b08.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 593751 3′. RC_AA206225_at zq56g08.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA clone 645662 3′. RC_D62834_at Human aorta cDNA 3′-end GEN-330D04. RC_D80981_at Human fetal brain cDNA 3′-end GEN-121E12. RC_H16772_at ym34g02.s1 Homo sapiens cDNA clone 50227 3′. RC_N62522_at yz74f08.s1 Homo sapiens cDNA clone 288807 3′. RC_N68222_at yz56e12.s1 Homo sapiens cDNA clone 287086 3′. RC_T10316_s_at seq1014 Homo sapiens cDNA clone b4HB3MA-COT8-HAP- Ft266 3′. RC_W37382_at zc12c07.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322092 3′. RC_W60582_at zd25e10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 341706 3′ similar to gb: M38188 OVARIAN GRANULOSA CELL 13,0 KD PROTEIN HGR74 (HUMAN);. RC_W84768_at zh53d03.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 415781 3′ similar to contains L1, b1 L1 repetitive element

In a preferred embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST.

AA011479_at zi01b10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429499 5′. AA314779_at EST186601 Colon carcinoma (HCC) cell line II Homo sapiens cDNA 5′ end. RC_AA084640_at zn20d05.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 547977 3′. RC_AA121534_at zk89d11.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 490005 3′ similar to gb: X79535 TUBULIN BETA-2 CHAIN (HUMAN);. RC_AA131047_s_(—) zo16f05.s1 Stratagene colon (#937204) Homo sapiens cDNA at clone 587073 3′. RC_AA461549_at zx62b09.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 796025 3′. RC_AA491465_at ab04a05.s1 Stratagene fetal retina 937202 Homo sapiens cDNA clone 839792 3′. RC_AA496936_at ae32d03.s1 Gessler Wilms tumor Homo sapiens cDNA clone 897509 3′. RC_AA598689_at ae49a08.s1 Stratagene lung carcinoma 937218 Homo sapiens cDNA clone 950198 3′. W26392_at 30g3 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA. RC_AA004887_at zh90g01.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 428592 3′. RC_AA135153_at zo24g02.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587858 3′. RC_AA197311_s_(—) zq50e09.s1 Stratagene neuroepithelium (#937231) Homo sapiens at cDNA clone 645064 3′ similar to gb: M24283 INTERCELLULAR ADHESION MOLECULE-1 PRECURSOR (HUMAN);. RC_H80622_at yu77b06.s1 Homo sapiens cDNA clone 239795 3′. RC_N64436_at za33a09.s1 Homo sapiens cDNA clone 294328 3′. RC_N67583_at yz42c02.s1 Homo sapiens cDNA clone 285698 3′. RC_R38678_at yc89d05.s1 Homo sapiens cDNA clone 23443 3′. RC_R56066_s_at yg91d08.s1 Homo sapiens cDNA clone 40992 3′. RC_R59292_at yh16a10.s1 Homo sapiens cDNA clone 37689 3′. RC_T24099_at seq2287 Homo sapiens cDNA clone Cot250Ft-b4HB3MA-8 3′. AA150364_at zl07b03.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491597 5′. AA174185_at PTH207 HTCDL1 Homo sapiens cDNA 5′/3′. AA452353_i_at zx15d05.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 786537 5′. AB002316_at Human mRNA for KIAA0318 gene, partial cds. H86858_at ys72d05.r1 Homo sapiens cDNA clone 220329 5′. M93119_s_at Human zinc-finger DNA-binding motifs (IA-1) mRNA, complete cds R72037_at yj86c09.r1 Homo sapiens cDNA clone 155632 5′. RC_AA004274_at zh97f02.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429243 3′ similar to contains element MER22 repetitive element;. RC_AA004415_at zh89b04.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 428431 3′. RC_AA007160_at 13cDNA30A-3,seq Soares infant brain 1NIB Homo sapiens cDNA clone HY18-3 3′. RC_AA053660_at zl74e07.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 510372 3′ similar to contains Alu repetitive element;. RC_AA252603_at zs14a11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 685148 3′. RC_AA411944_at zu03h01.s1 Soares testis NHT Homo sapiens cDNA clone 730801 3′. RC_AA412700_at zu12g03.s1 Soares testis NHT Homo sapiens cDNA clone 731668 3′. RC_AA430032_at zw65f05.s1 Soares testis NHT Homo sapiens cDNA clone 781089 3′. RC_AA430368_at zw20f06.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 769859 3′. RC_AA434113_at zw24b11.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 770205 3′ similar to contains element TAR1 repetitive element;. RC_AA441791_at zw62c02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774626 3′. RC_AA449419_at zx05b03.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 785549 3′. RC_AA449914_at zx37g02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 788690 3′. RC_D59847_at Human fetal brain cDNA 3′-end GEN-070G07. T95813_f_at ye45f10.r1 Homo sapiens cDNA clone 120715 5′ similar to gb: V00493_rna1 HEMOGLOBIN ALPHA CHAIN (HUMAN);. W80846_at zd83f05.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 347265 5′ similar to SW: SYB2_XENLA P47193 SYNAPTOBREVIN 2;. RC_AA031360_s_(—) zk16f07.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA at clone 470725 3′. RC_AA063624_at ze87h05.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366009 3′ similar to TR: G300372 G300372 CELL GROWTH REGULATING NUCLEOLAR PROTEIN, ;. RC_AA076238_at zm19e04.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 526110 3′ similar to contains Alu repetitive element;. RC_AA076350_at zm91a02.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 545258 3′. RC_AA101983_at zk87c02.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 489794 3′. RC_AA151245_at zl40f12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504431 3′. RC_AA164252_f_(—) zq46f06.s1 Stratagene hNT neuron (#937233) Homo sapiens at cDNA clone 632771 3′. RC_AA167006_at zo86b08.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 593751 3′. RC_AA206225_at zq56g08.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA clone 645662 3′. RC_D62834_at Human aorta cDNA 3′-end GEN-330D04. RC_D80981_at Human fetal brain cDNA 3′-end GEN-121E12. RC_H16772_at ym34g02.s1 Homo sapiens cDNA clone 50227 3′. RC_N62522_at yz74f08.s1 Homo sapiens cDNA clone 288807 3′. RC_N68222_at yz56e12.s1 Homo sapiens cDNA clone 287086 3′. RC_T10316_s_at seq1014 Homo sapiens cDNA clone b4HB3MA-COT8-HAP- Ft266 3′. RC_W37382_at zc12c07.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322092 3′. RC_W60582_at zd25e10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 341706 3′ similar to gb: M38188 OVARIAN GRANULOSA CELL 13.0 KD PROTEIN HGR74 (HUMAN);. RC_W84768_at zh53d03.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 415781 3′ similar to contains L1, b1 L1 repetitive element;.

In a preferred embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST.

AA203639_at zx58c10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 446706 5′ similar to contains Alu repetitive element;. M11844_at Human prealbumin gene, complete cds. RC_AA206042_at zq77f02.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA clone 647643 3′ similar to contains element MSR1 repetitive element;. RC_N51097_at yz03e04.s1 Homo sapiens cDNA clone 281982 3′. RC_H05527_at yl70f08.s1 Soares infant brain 1NIB Homo sapiens cDNA clone 43327 3′. AA115572_s_at zl05d11.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491445 5′ similar to TR: G895845 G895845 PUTATIVE P64 CLCP PROTEIN.;. RC_H12863_at yj14b12.s1 Homo sapiens cDNA clone 148703 3′. AA489287_at ab36e04.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842910 5′. RC_T96383_at ye49h07.s1 Homo sapiens cDNA clone 121117 3′. RC_H56453_at yq98g12.s1 Homo sapiens cDNA clone 203878 3′. RC_AA152194_at zl03h01.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491281 3′. RC_Z38520_at H. sapiens partial cDNA sequence; clone c-0ed05. RC_R38944_at yd06g09.s1 Homo sapiens cDNA clone 25061 3′ similar to contains Alu repetitive element;. RC_AA133926_at zo16e11.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587084 3′. RC_N69908_f_at za68f06.s1 Homo sapiens cDNA clone 297731 3′ similar to gb: X59244 ZINC FINGER PROTEIN 43 (HUMAN);. RC_AA151945_at zo02c02.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 566498 3′ similar to contains Alu repetitive element;. S83308_at SOX5 = Sry-related HMG box gene {alternatively spliced} [human. testis, mRNA, 1473 nt] RC_AA406570_at zv11b06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 753299 3′. RC_AA058314_at zl67g04.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 509718 3′ similar to contains Alu repetitive element; contains element PTR5 repetitive element;. RC_R98735_at yr31g12.s1 Homo sapiens cDNA clone 206950 3′.

In a preferred embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST.

RC_AA054726_at zk68e06.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 488002 3′. RC_AA206042_at zq77f02.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA clone 647643 3′ similar to contains element MSR1 repetitive element;. RC_R98735_at yr31g12.s1 Homo sapiens cDNA clone 206950 3′. AA115572_s_at zl05d11.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491445 5′ similar to TR: G895845 G895845 PUTATIVE P64 CLCP PROTEIN,;. AA430979_at PMY0789 KG1a Lambda Zap Express cDNA Library Homo sapiens cDNA 5′. AA489287_at ab36e04.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842910 5′. D82226_s_at similar to TAT-binding protein-2. H49499_s_at yq20g10.r1 Soares fetal liver spleen 1NFLS Homo sapiens cDNA clone 274386 5′. M11844_at Human prealbumin gene, complete cds. RC_AA026388_at ze92c03.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366436 3′. RC_AA044601_at zk55d05.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486729 3′. RC_AA182030_at zp57a03.s1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 624268 3′. RC_AA233451_at zr30b02.s1 Stratagene NT2 neuronal precursor 937230 Homo sapiens cDNA clone 664875 3′. RC_AA236493_at zr75c10.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 669234 3′. RC_AA401098_f_(—) zu50g01.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 741456 3′ similar to contains Alu repetitive element; contains element THR repetitive element;. RC_AA441818_at zw62f01.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774649 3′. RC_AA478109_at zt89d04.s1 Soares testis NHT Homo sapiens cDNA clone 729511 3′. RC_AA481430_at zv06g11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 752900 3′. RC_AA488878_at aa55f02.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 824859 3′. RC_AA599032_at ae41h03.s1 Gessler Wilms tumor Homo sapiens cDNA clone 898421 3′. S73288_at small proline-rich protein SPRK [human, odontogenic kerato- cysts, mRNA Partial, 317 nt]. U87459_at Human autoimmunogenic cancer/testis antigen NY-ESO-1 mRNA, complete cds U88047_at Human DNA binding protein homolog (DRX) mRNA, partial cds RC_AA063574_at ze25f03.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 360029 3′ similar to gb: X52104 P68 PROTEIN (HUMAN);. RC_AA132524_at zo20c04.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587430 3′ similar to contains Alu repetitive element;. RC_F09317_at H. sapiens partial cDNA sequence; clone c-2zh11. RC_H12863_at yj14b12.s1 Homo sapiens cDNA clone 148703 3′. RC_N33927_s_at yv25e09.s1 Homo sapiens cDNA clone 243784 3′. RC_R08189_at yf18f03.s1 Homo sapiens cDNA clone 127229 3′. RC_R39191_s_at yc89c12.s1 Homo sapiens cDNA clone 23345 3′. RC_T82323_at AS322 Homo sapiens cDNA clone AS322 3′. RC_T90746_at yd41f10.s1 Homo sapiens cDNA clone 110827 3′. RC_Z39338_at H. sapiens partial cDNA sequence; clone c-17f11.

In one embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST.

D80002_at Human mRNA for KIAA0180 gene, partial cds D82418_at similar to none. N28843_at yx59d10.r1 Homo sapiens cDNA clone 266035 5′. RC_F02541_at H. sapiens partial cDNA sequence; clone c-12c11. RC_N30806_at yw65f02.s1 Homo sapiens cDNA clone 257115 3′. RC_R33146_at yh81f02.s1 Homo sapiens cDNA clone 136155 3′ similar to contains Alu repetitive element;. RC_R40166_at yf70a09.s1 Homo sapiens cDNA clone 27448 3′. RC_R65998_at yi23g09.s1 Homo sapiens cDNA clone 140128 3′. RC_AA027823_at zk05c04.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 469638 3′. RC_AA084138_at zn17a03.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 547660 3′. RC_AA223902_at zr13a10.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA clone 648666 3′. RC_AA424524_at zv90g02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 767090 3′. RC_AA505136_at aa65d11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 825813 3′. AA043223_at zk55g12.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486790 5′.

In a preferred embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST

C01360_at HUMGS0008341, Human Gene Signature, 3′-directed cDNA sequence. D80002_at Human mRNA for KIAA0180 gene, partial cds RC_AA149586_at zl39e03.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504316 3′. RC_H68772_at yr83f01.s1 Homo sapiens cDNA clone 211897 3′. RC_N30806_at yw65f02.s1 Homo sapiens cDNA clone 257115 3′. RC_N63143_at yz37c12.s1 Homo sapiens cDNA clone 285238 3′. RC_R33146_at yh81f02.s1 Homo sapiens cDNA clone 136155 3′ similar to contains Alu repetitive element;. RC_R46206_at yj53d08.s1 Homo sapiens cDNA clone 152463 3′. RC_R49731_s_at yg71e10.s1 Homo sapiens cDNA clone 38554 3′. AA043223_at zk55g12.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486790 5′. AB002346_at Human mRNA for KIAA0348 gene, complete cds. D81608_at Human fetal brain cDNA 5′-end GEN-177B09. M83670_s_at Human carbonic anhydrase IV mRNA, complete cds N28843_at yx59d10.r1 Homo sapiens cDNA clone 266035 5′. RC_AA149044_at zl45d09.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504881 3′. RC_AA258130_at zs35f03.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 687197 3′. RC_AA281743_r_(—) zt06h05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone at IMAGE: 712377 3′. RC_AA406338_at zv10f06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 753251 3′. RC_AA424524_at zv90g02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 767090 3′. RC_AA435840_at zt80b08.s1 Soares testis NHT Homo sapiens cDNA clone 728631 3′. RC_AA027823_at zk05c04.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 469638 3′. RC_AA084138_at zn17a03.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 547660 3′. RC_AA135406_at zo28e08.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 588230 3′. RC_AA148923_at zl27g11.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 503204 3′. RC_H98653_at yx12h06.s1 Homo sapiens cDNA clone 261563 3′. RC_N30077_at yw81g11.s1 Homo sapiens cDNA clone 258692 3′. RC_R40166_at yf70a09.s1 Homo sapiens cDNA clone 27448 3′. RC_T90374_at yd43e03.s1 Homo sapiens cDNA clone 111004 3′similar to SP: POL2_MOUSE P11369 RETROVIRUS-RELATED POL POLYPROTEIN;. RC_Z38182_at H. sapiens partial cDNA sequence; clone c-02a08.

In another embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST.

RC_F03192_at H. sapiens partial cDNA sequence; clone c-1pb12. RC_W81552_at zd87g10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 347682 3′. RC_F02470_at H. sapiens partial cDNA sequence; clone c-10c01. RC_W44927_at zc20b06.s1 Scares senescent fibroblasts NbHSF Homo sapiens cDNA clone 322835 3′ similar to PIR: S44218 S44218 testin — mouse [1];. RC_R45292_at yg46b01.s1 Homo sapiens cDNA clone 35626 3′. RC_H62159_at yr47b09.s1 Homo sapiens cDNA clone 208409 3′ similar to contains Alu repetitive element; contains MER15 repetitive element;. RC_R17059_at yf45a10.s2 Homo sapiens cDNA clone 129786 3′. RC_H15259_at ym30c10.s1 Homo sapiens cDNA clone 49795 3′. W26376_at 29a6 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA. Y09616_at H. sapiens mRNA for putative carboxylesterase AA425593_at zw48f02.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 773307 5′. RC_AA279980_at zt08e05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 712544 3′. RC_H14089_at ym62c07.s1 Homo sapiens cDNA clone 163500 3′. RC_R46079_f_at yg49c02.s1 Homo sapiens cDNA clone 36133 3′. RC_W15360_at zc17d10.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322579 3′ similar to PIR: S39983 S39983 eps8 protein — mouse;. X52773_at Human mRNA for retinoic acid receptor-like protein RC_AA053886_s_(—) ze75b05.s1 Soares fetal heart NbHH19W Homo sapiens cDNA at clone 364785 3′ similar to TR: G451330 G451330 STEROL REGULATORY ELEMENT BINDING PROTEIN-2.;. RC_AA143493_at zo31a10.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 588474 3′. RC_Z98492_at Homo sapiens mRNA; expressed sequence tag; clone DKFZphsnu1_1b13, 3′ read. F15201_at H. sapiens partial cDNA sequence. RC_R61883_at yh10f08.s1 Homo sapiens cDNA clone 42872 3′. W26505_at 30e12 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA. RC_AA085676_at zn53e03.s1 Stratagene muscle 937209 Homo sapiens cDNA clone 561916 3′. AA018804_at ze55c07.r1 Soares retina N2b4HR Homo sapiens cDNA clone 362892 5′ similar to SW: RB14_RAT P35287 RAS-RELATED PROTEIN RAB-14. [1];. U22963_at Human class I histocompatibility antigen-like protein mRNA. complete cds. RC_R09230_at yf26d08.s1 Homo sapiens cDNA clone 127983 3′. RC_R67918_at yi25g01.s1 Homo sapiens cDNA clone 140304 3′. AA402119_at zu55d04.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 741895 5′ similar to TR: G397579 G397579 LL5 MRNA.;. AA082171_at zn42g07.r1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 550140 5′. R79750_at yi89d09.r1 Homo sapiens cDNA clone 146417 5′. RC_AA431773_at zw80d04.s1 Soares testis NHT Homo sapiens cDNA clone 782503 3′. RC_AA280670_at zs97a07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 711540 3′. AA303711_at EST16378 Aorta endothelial cells, TNF alpha-treated Homo sapiens cDNA 5′ end. AA400361_at zu64g03.r1 Soares testis NHT Homo sapiens cDNA clone 742804 5′. AF007111_at Homo sapiens MDM2-like p53-binding protein (MDMX) mRNA. complete cds. AA504384_at aa59c02.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 825218 5′ similar to contains element MIR repetitive element;. N88108_at K1565F Fetal heart, Lambda ZAP Express Homo sapiens cDNA clone K1565 5′ similar to EST(YD54C09.R1). RC_AA447769_at aa20e01.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 813816 3′.

In yet another preferred embodiment genes from the second gene group are selected individually from genes comprising sequences as identified below by EST.

AA402119_at zu55d04.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 741895 5′ similar to TR: G397579 G397579 LL5 MRNA,;, RC_AA102581_at zn42d02.s1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 550083 3′, RC_H14089_at ym62c07.s1 Homo sapiens cDNA clone 163500 3′, RC_R46079_f_at yg49c02.s1 Homo sapiens cDNA clone 36133 3′, RC_R67918_at yi25g01.s1 Homo sapiens cDNA clone 140304 3′, RC_W15360_at zc17d10.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322579 3′ similar to PIR: S39983 S39983 eps8 protein — mouse;, AA082171_at zn42g07.r1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 550140 5′, AA425593_at zw48f02.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 773307 5′, F15201_at H. sapiens partial cDNA sequence, H15219_at ym30f02.r1 Homo sapiens cDNA clone 49693 5′, R60368_at yh04b02.r1 Homo sapiens cDNA clone 42052 5′, R86859_at ym86a02.r1 Homo sapiens cDNA clone 165770 5′, RC_AA045342_at zk59g01.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 487152 3′, RC_AA171985_at zo98g05.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 594968 3′, T63174_s_at yc04e08.r1 Homo sapiens cDNA clone 79718 5′ similar to contains Alu repetitive element;, U90268_at Human Krit1 mRNA, complete cds, X14787_at Human mRNA for thrombospondin RC_AA196991_s_(—) zq10a10.s1 Stratagene muscle 937209 Homo sapiens cDNA at clone 629274 3′ similar to TR: G1049074 G1049074 VASOPRESSIN- ACTIVATED CALCIUM-MOBILIZING PROTEIN,;, RC_F02470_at H. sapiens partial cDNA sequence; clone c-10c01, RC_F08899_at H. sapiens partial cDNA sequence; clone c-2uc10, RC_H15259_at ym30c10.s1 Homo sapiens cDNA clone 49795 3′, RC_H52133_at yo44d04.s1 Homo sapiens cDNA clone 180775 3′, RC_R17059_at yf45a10.s2 Homo sapiens cDNA clone 129786 3′, RC_R45292_at yg46b01.s1 Homo sapiens cDNA clone 35626 3′,

The genes from the second gene group discussed above are preferably genes being expressed in all stages of the biological condition, such as all stages of a bladder tumor, to be used for determining the biological condition.

Particularly, the genes from the second gene group are selected individually from genes comprising sequences as identified below by EST, and which are associated with muscle invasive tumors.

RC_R00083_at ye73c08.s1 Homo sapiens cDNA clone 123374 3′. RC_R71391_at yj80e01.s1 Homo sapiens cDNA clone 155064 3′. RC_T23991_at seq2147 Homo sapiens cDNA clone NHB3MK-9 3′. RC_T79196_at yd70f06.s1 Homo sapiens cDNA clone 113603 3′ similar to contains Alu repetitive element;. RC_AA130596_(—) zo26a09.s1 Stratagene colon (#937204) Homo sapiens cDNA clone at 587992 3′. RC_AA459310_(—) zx89d06.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone r_at 810923 3′. RC_AA490965_(—) aa48f12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone at IMAGE: 824207 3′. U88047_at Human DNA binding protein homolog (DRX) mRNA, partial cds X56807_at Human DSC2 mRNA for desmocollins type 2a and 2b AA011479_at zi01b10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429499 5′. AA296821_at EST112387 Aorta endothelial cells Homo sapiens cDNA 5′ end.

Further, the genes from the second gene group are selected individually from genes comprising sequences as identified below by EST, and which are associated with solid tumors only.

RC_AA026418_at ze92h01.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366481 3′. RC_D59847_at Human fetal brain cDNA 3′-end GEN-070G07. RC_T24099_at seq2287 Homo sapiens cDNA clone Cot250Ft-b4HB3MA-8 3′. RC_R59292_at yh16a10.s1 Homo sapiens cDNA clone 37689 3′. RC_W60582_at zd25e10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 341706 3′ similar to gb: M38188 OVARIAN GRANULOSA CELL 13.0 KD PROTEIN HGR74 (HUMAN);. M63262_at Human 5-lipoxygenase activating protein (FLAP) gene RC_R38678_at yc89d05.s1 Homo sapiens cDNA clone 23443 3′. W60268_at zd29g01.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 342096 5′. AA465016_at zx80d02.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810051 5′ similar to TR: G1020091 G1020091 NEUROPSIN.; contains element LTR3 repetitive element;. RC_T79842_at yd83f04.s1 Homo sapiens cDNA clone 114847 3′. RC_AA206225_at zq56g08.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA clone 645662 3′. RC_AA449914_at zx37g02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 788690 3′. RC_F10211_at H. sapiens partial cDNA sequence; clone c-3bh08. RC_AA480109_r_at zv41f05.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 756225 3′ similar to TR: G498729 G498729 ZINC FINGER PROTEIN;. RC_AA053102_s_at zl72a06.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 5101303 3′. RC_AA434113_at zw24b11.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 770205 3′ similar to contains element TAR1 repetitive element;. RC_AA441791_at zw62c02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774626 3′. RC_N67583_at yz42c02.s1 Homo sapiens cDNA clone 285698 3′. RC_T96077_at ye47b12.s1 Homo sapiens cDNA clone 120863 3′. AB002316_at Human mRNA for KIAA0318 gene, partial cds. RC_W96222_at ze10g07.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 358620 3′. M16591_s_at Human hemopoietic cell protein-tyrosine kinase (HCK) gene, complete cds, clone lambda-a2/1a RC_N59808_at yz76b12.s1 Homo sapiens cDNA clone 288959 3′. RC_F10040_at H. sapiens partial cDNA sequence; clone c-39g09. RC_AA461549_at zx62b09.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 796025 3′. RC_W68683_at zd35d04.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 342631 3′. RC_AA084640_at zn20d05.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 547977 3′. C01169_at HUMGS0007858, Human Gene Signature, 3′-directed cDNA sequence. RC_AA491465_at ab04a05.s1 Stratagene fetal retina 937202 Homo sapiens cDNA clone 839792 3′. RC_W67564_s_at zd41c07.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 343212 3′. J03019_s_at Human beta-1-adrenergic receptor mRNA, complete cds. RC_H80622_at yu77b06.s1 Homo sapiens cDNA clone 239795 3′. RC_N34686_at yy15h06.s1 Homo sapiens cDNA clone 271355 3′. RC_R56066_s_at yg91d08.s1 Homo sapiens cDNA clone 40992 3′. RC_T34611_at EST71577 Homo sapiens cDNA 3′ end similar to None. RC_AA031373_s_at zk15e12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 470638 3′. X52056_at Human mRNA for spi-1 proto-oncogene N77564_at yz89g12.r1 Homo sapiens cDNA clone 290278 5′. C01765_at HUMGS0003713, Human Gene Signature, 3′-directed cDNA sequence. RC_AA496936_at ae32d03.s1 Gessler Wilms tumor Homo sapiens cDNA clone 897509 3′. RC_AA027103_at zk04e03.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 469564 3′. RC_R44131_at yg32c11.s1 Homo sapiens cDNA clone 34089 3′. RC_N67227_at yz48f04.s1 Homo sapiens cDNA clone 286303 3′. RC_T96677_at ye52f03.s1 Homo sapiens cDNA clone 121373 3′. RC_AA134965_i_at zo23g05.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587768 3′. RC_T86600_at yd87d10.s1 Homo sapiens cDNA clone 115219 3′. RC_AA054087_at zf51f03.s1 Soares retina N2b4HR Homo sapiens cDNA clone 380477 3′. AA444374_at zv76b10.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA 5′. RC_H72357_at ys04f01.s1 Homo sapiens cDNA clone 213817 3′ similar to gb: J04970 CARBOXYPEPTIDASE M PRECURSOR (HUMAN); contains Alu repetitive element;. RC_AA017045_at ze37d11.s1 Soares retina N2b4HR Homo sapiens cDNA clone 361173 3′. AA010324_at zi09c03.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 430276 5′. RC_AA234743_at zs38b09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 687449 3′. RC_AA055892_at zf20d06.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 377483 3′. RC_AA446650_at zw89g02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 784178 3′. H91747_s_at ys80e03.r1 Homo sapiens cDNA clone 221116 5′. AA401510_s_at zu63c08.r1 Soares testis NHT Homo sapiens cDNA clone 742670 5′. RC_W61239_at zd31d10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 342259 3′.

In another embodiment the genes from the second gene group are selected individually from genes comprising sequences as identified below by EST, and which are associated with mixed tumors comprising both solid and papilloma elements of invasive type.

AA203639_at zx58c10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 446706 5′ similar to contains Alu repetitive element;. M11844_at Human prealbumin gene, complete cds. RC_AA206042_at zq77f02.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA clone 647643 3′ similar to contains element MSR1 repetitive element;. RC_N51097_at yz03e04.s1 Homo sapiens cDNA clone 281982 3′. RC_H05527_at yl70f08.s1 Soares infant brain 1NIB Homo sapiens cDNA clone 43327 3′. AA115572_s_at zl05d11.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491445 5′ similar to TR: G895845 G895845 PUTATIVE P64 CLCP PROTEIN.;. RC_H12863_at yj14b12.s1 Homo sapiens cDNA clone 148703 3′. AA489287_at ab36e04.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842910 5′. RC_T96383_at ye49h07.s1 Homo sapiens cDNA clone 121117 3′. RC_H56453_at yq98g12.s1 Homo sapiens cDNA clone 203878 3′. RC_AA152194_at zl03h01.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491281 3′. RC_Z38520_at H. sapiens partial cDNA sequence; clone c-0ed05. RC_R38944_at yd06g09.s1 Homo sapiens cDNA clone 25061 3′ similar to contains Alu repetitive element;. RC_AA133926_at zo16e11.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587084 3′. RC_N69908_f_at za68f06.s1 Homo sapiens cDNA clone 297731 3′ similar to gb: X59244 ZINC FINGER PROTEIN 43 (HUMAN);. RC_AA151945_at zo02c02.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 566498 3′ similar to contains Alu repetitive element;. S83308_at SOX5 = Sry-related HMG box gene {alternatively spliced} [human, testis, mRNA, 1473 nt] RC_AA406570_at zv11b06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 753299 3′. RC_AA058314_at zl67g04.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 509718 3′ similar to contains Alu repetitive element; contains element PTR5 repetitive element;. RC_R98735_at yr31g12.s1 Homo sapiens cDNA clone 206950 3′.

More particularly the genes from the second gene group are selected individually from genes comprising sequences as identified below by EST, and which are associated with T1 tumors (mucosa invasive tumor)

D80002_at Human mRNA for KIAA0180 gene, partial cds D82418_at similar to none. N28843_at yx59d10.r1 Homo sapiens cDNA clone 266035 5′. RC_F02541_(—) H. sapiens partial cDNA sequence; clone c-12c11. at RC_N30806_(—) yw65f02.s1 Homo sapiens cDNA clone 257115 3′. at RC_R33146_(—) yh81f02.s1 Homo sapiens cDNA clone 136155 3′ similar to contains at Alu repetitive element;. RC_R40166_(—) yf70a09.s1 Homo sapiens cDNA clone 27448 3′. at RC_R65998_(—) yi23g09.s1 Homo sapiens cDNA clone 140128 3′. at RC_AA027823_(—) zk05c04.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA at clone 469638 3′. RC_AA084138_(—) zn17a03.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo at sapiens cDNA clone 547660 3′. RC_AA223902_(—) zr13a10.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA at clone 648666 3′. RC_AA424524_(—) zv90g02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 767090 at 3′. RC_AA505136_(—) aa65d11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone at IMAGE: 825813 3′. AA043223_at zk55g12.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486790 5′.

Even more particularly the genes from the second gene group are selected individually from genes comprising sequences as identified below by EST, and which are associated with superficial Ta tumors.

RC_F03192_at H. sapiens partial cDNA sequence; clone c-1pb12. RC_W81552_at zd87g10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 347682 3′. RC_F02470_at H. sapiens partial cDNA sequence; clone c-10c01. RC_W44927_at zc20b06.s1 Soares senescent fibroblasts NbHSF Homo sapiens cDNA clone 322835 3′ similar to PIR: S44218 S44218 testin - mouse [1];. RC_R45292_at yg46b01.s1 Homo sapiens cDNA clone 35626 3′. RC_H62159_at yr47b09.s1 Homo sapiens cDNA clone 208409 3′ similar to contains Alu repetitive element; contains MER15 repetitive element;. RC_R17059_at yf45a10.s2 Homo sapiens cDNA clone 129786 3′. RC_H15259_at ym30c10.s1 Homo sapiens cDNA clone 49795 3′. W26376_at 29a6 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA. Y09616_at H. sapiens mRNA for putative carboxylesterase AA425593_at zw48f02.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 773307 5′. RC_AA279980_at zt08e05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 712544 3′. RC_H14089_at ym62c07.s1 Homo sapiens cDNA clone 163500 3′. RC_R46079_f_at yg49c02.s1 Homo sapiens cDNA clone 36133 3′. RC_W15360_at zc17d10.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322579 3′ similar to PIR: S39983 S39983 eps8 protein - mouse;. X52773_at Human mRNA for retinoic acid receptor-like protein RC_AA053886_s_(—) ze75b05.s1 Soares fetal heart NbHH19W Homo sapiens cDNA at clone 364785 3′ similar to TR: G451330 G451330 STEROL REGULATORY ELEMENT BINDING PROTEIN-2.;. RC_AA143493_at zo31a10.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 588474 3′. RC_Z98492_at Homo sapiens mRNA; expressed sequence tag; clone DKFZphsnu1_1b13, 3′ read. F15201_at H. sapiens partial cDNA sequence. RC_R61883_at yh10f08.s1 Homo sapiens cDNA clone 42872 3′. W26505_at 30e12 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA. RC_AA085676_at zn53e03.s1 Stratagene muscle 937209 Homo sapiens cDNA clone 561916 3′. AA018804_at ze55c07.r1 Soares retina N2b4HR Homo sapiens cDNA clone 362892 5′ similar to SW: RB14_RAT P35287 RAS-RELATED PROTEIN RAB-14. [1];. U22963_at Human class I histocompatibility antigen-like protein mRNA, complete cds. RC_R09230_at yf26d08.s1 Homo sapiens cDNA clone 127983 3′. RC_R67918_at yi25g01.s1 Homo sapiens cDNA clone 140304 3′. AA402119_at zu55d04.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 741895 5′ similar to TR: G397579 G397579 LL5 MRNA.;. AA082171_at zn42g07.r1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 550140 5′. R79750_at yi89d09.r1 Homo sapiens cDNA clone 146417 5′. RC_AA431773_at zw80d04.s1 Soares testis NHT Homo sapiens cDNA clone 782503 3′. RC_AA280670_at zs97a07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 711540 3′. AA303711_at EST16378 Aorta endothelial cells, TNF alpha-treated Homo sapiens cDNA 5′ end. AA400361_at zu64g03.r1 Soares testis NHT Homo sapiens cDNA clone 742804 5′. AF007111_at Homo sapiens MDM2-like p53-binding protein (MDMX) mRNA, complete cds. AA504384_at aa59c02.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 825218 5′ similar to contains element MIR repetitive element;. N88108_at K1565F Fetal heart, Lambda ZAP Express Homo sapiens cDNA clone K1565 5′ similar to EST(YD54C09.R1). RC_AA447769_at aa20e01.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 813816 3′.

More particularly the genes from the second gene group are selected individually from genes comprising sequences as identified below by EST, and which are associated with T1 tumors (mucosa invasive tumor).

D80002_at Human mRNA for KIAA0180 gene, partial cds D82418_at similar to none. N28843_at yx59d10.r1 Homo sapiens cDNA clone 266035 5′. RC_F02541_(—) H. sapiens partial cDNA sequence; clone c-12c11. at RC_N30806_(—) yw65f02.s1 Homo sapiens cDNA clone 257115 3′. at RC_R33146_(—) yh81f02.s1 Homo sapiens cDNA clone 136155 3′ similar to contains at Alu repetitive element;. RC_R40166_(—) yf70a09.s1 Homo sapiens cDNA clone 27448 3′. at RC_R65998_(—) yi23g09.s1 Homo sapiens cDNA clone 140128 3′. at RC_AA027823_(—) zk05c04.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA at clone 469638 3′. RC_AA084138_(—) zn17a03.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo at sapiens cDNA clone 547660 3′. RC_AA223902_(—) zr13a10.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA at clone 648666 3′. RC_AA424524_(—) zv90g02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 767090 at 3′. RC_AA505136_(—) aa65d11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone at IMAGE: 825813 3′. AA043223_at zk55g12.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486790 5′. Number of Genes

As discussed above, it is possible to use a single gene approach determining the expression of one of the genes only, in order to determine the biological condition of the tissue. It is however preferred that expression from at least one gene from the first group, such as at least two, for example at least three, such as at least four, such as at least five, such as more than six genes are determined as well as expression from at least one gene from the second group, such as at least two, for example at least three, such as at least four, such as at least five, such as more than six genes are determined to obtain a more statistically significant result, that is more independent of the expression level of the individual gene.

In one embodiment expression from more genes from both groups are determined, such as determination of expression from at least two genes from either of the gene groups, such as determination of expression from at least three genes from either of the gene groups, such as determination of expression from at least four genes from either of the gene groups, such as determination of expression from at least five genes from either of the gene groups, such as determination of expression from at least six genes from either of the gene groups, such as determination of expression from at least seven genes from either of the gene groups.

A pattern of characteristic expression of one gene can be useful in characterizing a cell type source or a stage of disease. However, more genes may be usefully analyzed. Useful patterns include expression of at least one, two, three, five, ten, fifteen, twenty, twenty-five, fifty, seventy-five, one hundred or several hundred informative genes.

Expression Level

Using the results provided in the accompanying figures, a gene is indicated as being expressed if an intensity value of greater than or equal to 20 or scored as P=present by the software is shown. Conversely, an intensity value of less than 20 or scored as A=absent indicates that the gene is not expressed above background levels. Comparison of an expression pattern to another may score a change from expressed to non-expressed, or the reverse. Alternatively, changes in intensity of expression may be scored, either increases or decreases. Any significant change can be used. Typical changes which are more than 2-fold are suitable. Changes which are greater than 5-fold are highly suitable.

The present invention in particular relates to methods using genes wherein the ratio of the expression level in normal tissue to biological condition tissue for suppressor genes or vice versa of the expression level in biological condition tissue to normal tissue for condition genes is as high as possible, such as at least a two-fold change in expression, such as at least a three-fold change, for example at least a four fold change, such as at least a five fold change, for example at least a six fold change, such as at least a ten fold change, for example at least a fifteen fold change, such as at least a twenty fold change.

Stages and Grades

Stage of a bladder tumor indicates how deep the tumor has penetrated. Superficial tumors are termed Ta, T1, T2, T3 and T4 are used to describe increasing degrees of penetration into the muscle. The grade of a bladder tumor is expressed on a scale of I-IV (1-4) according to Bergkvist, A.; Ijungquist, A.; Moberger, B. “Classification of bladder tumours basedf on the cellular pattern. Preliminary report of a clinical-pathological study of 300 cases with a minimum follow-up of eight years”, Acta Chir Scand., 1965, 130(4):371-8). The grade reflects the cytological appearance of the cells. Grade I cells are almost normal. Grade II cells are slightly deviant. Grade III cells are clearly abnormal. And Grade IV cells are highly abnormal. A special form of bladder malignancy is carcinoma-in-situ or dyplasia-in-situ in which the altered cells are located in-situ.

It is important to classify the stage of a cancer disease, as superficial tumors may require a less intensive treatment than invasive tumors. According to the invention the expression level of genes may be used to identify genes whose expression can be used to identify a certain stage of the disease. These “Classifiers” are divided into those which can be used to identify Ta, T2, T3, and T4 stages. In one aspect of the invention measuring the transcript level of one or more of these genes may lead to a classifier that can add supplementary information to the information obtained from the pathological T2 classification. For example gene expression levels that signify a T2 will be unfavourable to detect in a Ta tumor, as they may signal that the Ta tumor has the potential to become a T2 tumor. The opposite is probably also true, that an expression level that signify Ta will be favorable to have in a T2 tumor. In that way independent information may be obtained from T2-T4 pathological classification and a classification based on gene expression levels is made.

The method of determining the stage of a tumor may be combined with determination of the biological condition or may be an independent method as such. The difference in expression level of a gene from one stage to the expression level of the gene in another group is preferably at least two-fold, such as at least three-fold.

Thus, the invention relates to a method of determining the stage of a bladder tumor, wherein the stage is selected from bladder cancer stages Ta, T1; T2, T3 and T4 comprising assaying at least the expression of Ta stage gene from a Ta stage gene group, at least one expression of T1 stage gene from a T1 stage gene group, at least the expression of T2 stage gene from a T2 stage gene group, at least the expression of T3 stage gene from a T3 stage gene group, at least the expression of T4 stage gene from a T4 stage gene group wherein at least one gene from each gene group is expressed in a significantly different amount in that stage than in one of the other stages.

Preferably, the genes selected may be a gene from each gene group being expressed in a significantly higher amount in that stage than in one of the other stages, such as:

-   a Ta stage gene selected individually from any gene comprising a     sequence as identified below as EST

RC_F03192_at H. sapiens partial cDNA sequence; clone c-1pb12. RC_W81552_at zd87g10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 347682 3′. RC_F02470_at H. sapiens partial cDNA sequence; clone c-10c01. RC_W44927_at zc20b06.s1 Soares senescent fibroblasts NbHSF Homo sapiens cDNA clone 322835 3′ similar to PIR: S44218 S44218 testin - mouse [1];. RC_R45292_at yg46b01.s1 Homo sapiens cDNA clone 35626 3′. RC_H62159_at yr47b09.s1 Homo sapiens cDNA clone 208409 3′ similar to contains Alu repetitive element; contains MER15 repetitive element;. RC_R17059_at yf45a10.s2 Homo sapiens cDNA clone 129786 3′. RC_H15259_at ym30c10.s1 Homo sapiens cDNA clone 49795 3′. W26376_at 29a6 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA. Y09616_at H. sapiens mRNA for putative carboxylesterase AA425593_at zw48f02.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 773307 5′. RC_AA279980_at zt08e05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 712544 3′. RC_H14089_at ym62c07.s1 Homo sapiens cDNA clone 163500 3′. RC_R46079_f_at yg49c02.s1 Homo sapiens cDNA clone 36133 3′. RC_W15360_at zc17d10.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322579 3′ similar to PIR: S39983 S39983 eps8 protein - mouse;. X52773_at Human mRNA for retinoic acid receptor-like protein RC_AA053886_s_at ze75b05.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 364785 3′ similar to TR: G451330 G451330 STEROL REGULATORY ELEMENT BINDING PROTEIN-2.;. RC_AA143493_at zo31a10.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 588474 3′. RC_Z98492_at Homo sapiens mRNA; expressed sequence tag; clone DKFZphsnu1_1b13 3′ read. F15201_at H. sapiens partial cDNA sequence. RC_R61883_at yh10f08.s1 Homo sapiens cDNA clone 42872 3′. W26505_at 30e12 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA. RC_AA085676_at zn53e03.s1 Stratagene muscle 937209 Homo sapiens cDNA clone 561916 3′. AA018804_at ze55c07.r1 Soares retina N2b4HR Homo sapiens cDNA clone 362892 5′ similar to SW: RB14_RAT P35287 RAS-RELATED PROTEIN RAB-14. [1];. U22963_at Human class I histocompatibility antigen-like protein mRNA, complete cds. RC_R09230_at yf26d08.s1 Homo sapiens cDNA clone 127983 3′. RC_R67918_at yi25g01.s1 Homo sapiens cDNA clone 140304 3′. AA402119_at zu55d04.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 741895 5′ similar to TR: G397579 G397579 LL5 MRNA.;. AA082171_at zn42g07.r1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 550140 5′. R79750_at yi89d09.r1 Homo sapiens cDNA clone 146417 5′. RC_AA431773_at zw80d04.s1 Soares testis NHT Homo sapiens cDNA clone 782503 3′. RC_AA280670_at zs97a07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 711540 3′. AA303711_at EST16378 Aorta endothelial cells, TNF alpha-treated Homo sapiens cDNA 5′ end. AA400361_at zu64g03.r1 Soares testis NHT Homo sapiens cDNA clone 742804 5′. AF007111_at Homo sapiens MDM2-like p53-binding protein (MDMX) mRNA, complete cds. AA504384_at aa59c02.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 825218 5′ similar to contains element MIR repetitive element;. N88108_at K1565F Fetal heart, Lambda ZAP Express Homo sapiens cDNA clone K1565 5′ similar to EST(YD54C09.R1). RC_AA447769_at aa20e01.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 813816 3′. or a sequence as identified below

UniGene number Homologous to AA402119_at Zu55d04.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 741895 5′ similar to TR: G397579 G397579 LL5 MRNA.;, RC_AA102581_at Zn42d02.s1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 550083 3′, RC_H14089_at Ym62c07.s1 Homo sapiens cDNA clone 163500 3′, RC_R46079_f_at Yg49c02.s1 Homo sapiens cDNA clone 36133 3′, RC_R67918_at Yi25g01.s1 Homo sapiens cDNA clone 140304 3′, RC_W15360_at Zc17d10.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322579 3′ similar to PIR: S39983 S39983 eps8 protein - mouse;, AA082171_at Zn42g07.r1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 550140 5′, AA425593_at Zw48f02.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 773307 5′, F15201_at H. sapiens partial cDNA sequence, H15219_at Ym30f02.r1 Homo sapiens cDNA clone 49693 5′, R60368_at Yh04b02.r1 Homo sapiens cDNA clone 42052 5′, R86859_at Ym86a02.r1 Homo sapiens cDNA clone 165770 5′, RC_AA045342_at Zk59g01.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 487152 3′, RC_AA171985_at Zo98g05.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 594968 3′, T63174_s_at Yc04e08.r1 Homo sapiens cDNA clone 79718 5′ similar to contains Alu repetitive element;, U90268_at Human Krit1 mRNA, complete cds, X14787_at Human mRNA for thrombospondin RC_AA196991_s_(—) Zq10a10.s1 Stratagene muscle 937209 Homo sapiens cDNA at clone 629274 3′ similar to TR: G1049074 G1049074 VASOPRESSIN- ACTIVATED CALCIUM-MOBILIZING PROTEIN.;, RC_F02470_at H. sapiens partial cDNA sequence; clone c-10c01, RC_F08899_at H. sapiens partial cDNA sequence; clone c-2uc10, RC_H15259_at Ym30c10.s1 Homo sapiens cDNA clone 49795 3′, RC_H52133_at Yo44d04.s1 Homo sapiens cDNA clone 180775 3′, RC_R17059_at Yf45a10.s2 Homo sapiens cDNA clone 129786 3′, RC_R45292_at Yg46b01.s1 Homo sapiens cDNA clone 35626 3′,

More preferably, a T1 stage gene is selected individually from any gene comprising a sequence as identified below

D80002_at Human mRNA for KIAA0180 gene, partial cds D82418_at similar to none. N28843_at yx59d10.r1 Homo sapiens cDNA clone 266035 5′. RC_F02541_at H. sapiens partial cDNA sequence; clone c-12c11. RC_N30806_at yw65f02.s1 Homo sapiens cDNA clone 257115 3′. RC_R33146_at yh81f02.s1 Homo sapiens cDNA clone 136155 3′ similar to contains Alu repetitive element;. RC_R40166_at yf70a09.s1 Homo sapiens cDNA clone 27448 3′. RC_R65998_at yi23g09.s1 Homo sapiens cDNA clone 140128 3′. RC_AA027823_at zk05c04.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 469638 3′. RC_AA084138_at zn17a03.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 547660 3′. RC_AA223902_at zr13a10.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA clone 648666 3′. RC_AA424524_at zv90g02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 767090 3′. RC_AA505136_at aa65d11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 825813 3′. AA043223_at zk55g12.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486790 5′. or a sequence as identified below

UniGene number Homologous to C01360_at HUMGS0008341, Human Gene Signature, 3′-directed cDNA sequence, D80002_at Human mRNA for KIAA0180 gene, partial cds RC_AA149586_at Zl39e03.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504316 3′, RC_H68772_at Yr83f01.s1 Homo sapiens cDNA clone 211897 3′, RC_N30806_at Yw65f02.s1 Homo sapiens cDNA clone 257115 3′, RC_N63143_at Yz37c12.s1 Homo sapiens cDNA clone 285238 3′, RC_R33146_at Yh81f02.s1 Homo sapiens cDNA clone 136155 3′ similar to contains Alu repetitive element;, RC_R46206_at Yj53d08.s1 Homo sapiens cDNA clone 152463 3′, RC_R49731_s_at Yg71e10.s1 Homo sapiens cDNA clone 38554 3′, AA043223_at Zk55g12.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486790 5′, AB002346_at Human mRNA for KIAA0348 gene, complete cds, D81608_at Human fetal brain cDNA 5′-end GEN-177B09, M83670_s_at Human carbonic anhydrase IV mRNA, complete cds N28843_at Yx59d10.r1 Homo sapiens cDNA clone 266035 5′, RC_AA149044_at Zl45d09.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504881 3′, RC_AA258130_at Zs35f03.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 687197 3′, RC_AA281743_r_(—) Zt06h05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone at IMAGE: 712377 3′, RC_AA406338_at Zv10f06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 753251 3′, RC_AA424524_at Zv90g02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 767090 3′, RC_AA435840_at Zt80b08.s1 Soares testis NHT Homo sapiens cDNA clone 728631 3′, RC_AA027823_at Zk05c04.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 469638 3′, RC_AA084138_at Zn17a03.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 547660 3′, RC_AA135406_at Zo28e08.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 588230 3′, RC_AA148923_at Zl27g11.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 503204 3′, RC_H98653_at Yx12h06.s1 Homo sapiens cDNA clone 261563 3′, RC_N30077_at Yw81g11.s1 Homo sapiens cDNA clone 258692 3′, RC_R40166_at Yf70a09.s1 Homo sapiens cDNA clone 27448 3′, RC_T90374_at Yd43e03.s1 Homo sapiens cDNA clone 111004 3′ similar to SP: POL2_MOUSE P11369 RETROVIRUS-RELATED POL POLYPROTEIN;, RC_Z38182_at H. sapiens partial cDNA sequence; clone c-02a08,

In yet another preferred embodiment a T2-T4 stage gene is selected individually from any gene comprising a sequence as identified below

RC_R00083_at ye73c08.s1 Homo sapiens cDNA clone 123374 3′. RC_R71391_at yj80e01.s1 Homo sapiens cDNA clone 155064 3′. RC_T23991_at seq2147 Homo sapiens cDNA clone NHB3MK-9 3′. RC_T79196_at yd70f06.s1 Homo sapiens cDNA clone 113603 3′ similar to contains Alu repetitive element;. RC_AA130596_at zo26a09.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587992 3′. RC_AA459310_r_(—) zx89d06.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 810923 3′. RC_AA490965_at aa48f12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 824207 3′. U88047_at Human DNA binding protein homolog (DRX) mRNA, partial cds X56807_at Human DSC2 mRNA for desmocollins type 2a and 2b AA011479_at zi01b10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429499 5′. AA296821_at EST112387 Aorta endothelial cells Homo sapiens cDNA 5′ end. or a sequence as identified below

RC_AA054726_at Zk68e06.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 488002 3′, RC_AA206042_at Zq77f02.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA clone 647643 3′ similar to contains element MSR1 repetitive element;, RC_R98735_at Yr31g12.s1 Homo sapiens cDNA clone 206950 3′, AA115572_s_at Zl05d11.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491445 5′ similar to TR: G895845 G895845 PUTATIVE P64 CLCP PROTEIN,;, AA430979_at PMY0789 KG1a Lambda Zap Express cDNA Library Homo sapiens cDNA 5′, AA489287_at ab36e04.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842910 5′, D82226_s_at similar to TAT-binding protein-2, H49499_s_at yq20g10.r1 Soares fetal liver spleen 1NFLS Homo sapiens cDNA clone 274386 5′, M11844_at Human prealbumin gene, complete cds, RC_AA026388_at ze92c03.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366436 3′, RC_AA044601_at zk55d05.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 486729 3′, RC_AA182030_at zp57a03.s1 Stratagene endothelial cell 937223 Homo sapiens cDNA clone 624268 3′, RC_AA233451_at zr30b02.s1 Stratagene NT2 neuronal precursor 937230 Homo sapiens cDNA clone 664875 3′, RC_AA236493_at zr75c10.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 669234 3′, RC_AA401098_f_(—) zu50g01.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 741456 3′ similar to contains Alu repetitive element; contains element THR repetitive element;, RC_AA441818_at zw62f01.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774649 3′, RC_AA478109_at zt89d04.s1 Soares testis NHT Homo sapiens cDNA clone 729511 3′, RC_AA481430_at zv06g11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 752900 3′, RC_AA488878_at aa55f02.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 824859 3′, RC_AA599032_at ae41h03.s1 Gessler Wilms tumor Homo sapiens cDNA clone 898421 3′, S73288_at small proline-rich protein SPRK [human, odontogenic keratocysts, mRNA Partial, 317 nt], U87459_at Human autoimmunogenic cancer/testis antigen NY-ESO-1 mRNA, complete cds U88047_at Human DNA binding protein homolog (DRX) mRNA, partial cds RC_AA063574_at ze25f03.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 360029 3′ similar to gb: X52104 P68 PROTEIN (HUMAN);, RC_AA132524_at zo20c04.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587430 3′ similar to contains Alu repetitive element;, RC_F09317_at H. sapiens partial cDNA sequence; clone c-2zh11, RC_H12863_at yj14b12.s1 Homo sapiens cDNA clone 148703 3′, RC_N33927_s_at yv25e09.s1 Homo sapiens cDNA clone 243784 3′, RC_R08189_at yf18f03.s1 Homo sapiens cDNA clone 127229 3′, RC_R39191_s_at yc89c12.s1 Homo sapiens cDNA clone 23345 3′, RC_T82323_at AS322 Homo sapiens cDNA clone AS322 3′, RC_T90746_at yd41f10.s1 Homo sapiens cDNA clone 110827 3′, RC_Z39338_at H. sapiens partial cDNA sequence; clone c-17f11, or preferably any gene comprising a sequence as identified below

AA011479_at zi01b10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429499 5′, AA314779_at EST186601 Colon carcinoma (HCC) cell line II Homo sapiens cDNA 5′ end, RC_AA084640_at zn20d05.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone 547977 3′, RC_AA121534_at zk89d11.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 490005 3′ similar to gb: X79535 TUBULIN BETA-2 CHAIN (HUMAN);, RC_AA131047_s_(—) zo16f05.s1 Stratagene colon (#937204) Homo sapiens cDNA at clone 587073 3′, RC_AA461549_at zx62b09.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 796025 3′, RC_AA491465_at ab04a05.s1 Stratagene fetal retina 937202 Homo sapiens cDNA clone 839792 3′, RC_AA496936_at ae32d03.s1 Gessler Wilms tumor Homo sapiens cDNA clone 897509 3′, RC_AA598689_at ae49a08.s1 Stratagene lung carcinoma 937218 Homo sapiens cDNA clone 950198 3′, W26392_at 30g3 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA, RC_AA004887_at zh90g01.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 428592 3′, RC_AA135153_at zo24g02.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587858 3′, RC_AA197311_s_(—) zq50e09.s1 Stratagene neuroepithelium (#937231) Homo sapiens at cDNA clone 645064 3′ similar to gb: M24283 INTERCELLULAR ADHESION MOLECULE-1 PRECURSOR (HUMAN);, RC_H80622_at yu77b06.s1 Homo sapiens cDNA clone 239795 3′, RC_N64436_at za33a09.s1 Homo sapiens cDNA clone 294328 3′, RC_N67583_at yz42c02.s1 Homo sapiens cDNA clone 285698 3′, RC_R38678_at yc89d05.s1 Homo sapiens cDNA clone 23443 3′, RC_R56066_s_at yg91d08.s1 Homo sapiens cDNA clone 40992 3′, RC_R59292_at yh16a10.s1 Homo sapiens cDNA clone 37689 3′, RC_T24099_at seq2287 Homo sapiens cDNA clone Cot250Ft-b4HB3MA-8 3′, AA150364_at zl07b03.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491597 5′, AA174185_at PTH207 HTCDL1 Homo sapiens cDNA 5′/3′, AA452353_i_at zx15d05.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 786537 5′, AB002316_at Human mRNA for KIAA0318 gene, partial cds, H86858_at ys72d05.r1 Homo sapiens cDNA clone 220329 5′, M93119_s_at Human zinc-finger DNA-binding motifs (IA-1) mRNA, complete cds R72037_at yj86c09.r1 Homo sapiens cDNA clone 155632 5′, RC_AA004274_at zh97f02.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429243 3′ similar to contains element MER22 repetitive element;, RC_AA004415_at zh89b04.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 428431 3′, RC_AA007160_at 13cDNA30A-3,seq Soares infant brain 1NIB Homo sapiens cDNA clone HY18-3 3′, RC_AA053660_at zl74e07.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 510372 3′ similar to contains Alu repetitive element;, RC_AA252603_at zs14a11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 685148 3′, RC_AA411944_at zu03h01.s1 Soares testis NHT Homo sapiens cDNA clone 730801 3′, RC_AA412700_at zu12g03.s1 Soares testis NHT Homo sapiens cDNA clone 731668 3′, RC_AA430032_at zw65f05.s1 Soares testis NHT Homo sapiens cDNA clone 781089 3′, RC_AA430368_at zw20f06.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 769859 3′, RC_AA434113_at zw24b11.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 770205 3′ similar to contains element TAR1 repetitive element;, RC_AA441791_at zw62c02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774626 3′, RC_AA449419_at zx05b03.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 785549 3′, RC_AA449914_at zx37g02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 788690 3′, RC_D59847_at Human fetal brain cDNA 3′-end GEN-070G07, T95813_f_at ye45f10.r1 Homo sapiens cDNA clone 120715 5′ similar to gb: V00493_rna1 HEMOGLOBIN ALPHA CHAIN (HUMAN);, W80846_at zd83f05.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 347265 5′ similar to SW: SYB2_XENLA P47193 SYNAP- TOBREVIN 2;, RC_AA031360_s_(—) zk16f07.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA at clone 470725 3′, RC_AA063624_at ze87h05.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366009 3′ similar to TR: G300372 G300372 CELL GROWTH REGULATING NUCLEOLAR PROTEIN,;, RC_AA076238_at zm19e04.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 526110 3′ similar to contains Alu repetitive element;, RC_AA076350_at zm91a02.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 545258 3′, RC_AA101983_at zk87c02.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 489794 3′, RC_AA151245_at zl40f12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 504431 3′, RC_AA164252_f_(—) zq46f06.s1 Stratagene hNT neuron (#937233) Homo sapiens at cDNA clone 632771 3′, RC_AA167006_at zo86b08.s1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 593751 3′, RC_AA206225_at zq56g08.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA clone 645662 3′, RC_D62834_at Human aorta cDNA 3′-end GEN-330D04, RC_D80981_at Human fetal brain cDNA 3′-end GEN-121E12, RC_H16772_at ym34g02.s1 Homo sapiens cDNA clone 50227 3′, RC_N62522_at yz74f08.s1 Homo sapiens cDNA clone 288807 3′, RC_N68222_at yz56e12.s1 Homo sapiens cDNA clone 287086 3′, RC_T10316_s_at seq1014 Homo sapiens cDNA clone b4HB3MA-COT8-HAP- Ft266 3′, RC_W37382_at zc12c07.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322092 3′, RC_W60582_at zd25e10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 341706 3′ similar to gb: M38188 OVARIAN GRANULOSA CELL 13,0 KD PROTEIN HGR74 (HUMAN);, RC_W84768_at zh53d03.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 415781 3′ similar to contains L1,b1 L1 repetitive element;, or a sequence as identified below expressed in solid tumors

RC_AA026418_at ze92h01.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366481 3′ . RC_D59847_at Human fetal brain cDNA 3′-end GEN-070G07. RC_T24099_at seq2287 Homo sapiens cDNA clone Cot250Ft-b4HB3MA-8 3′. RC_R59292_at yh16a10.s1 Homo sapiens cDNA clone 37689 3′. RC_W60582_at zd25e10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 341706 3′ similar to gb: M38188 OVARIAN GRANULOSA CELL 13.0 KD PROTEIN HGR74 (HUMAN);. M63262_at Human 5-lipoxygenase activating protein (FLAP) gene RC_R38678_at yc89d05.s1 Homo sapiens cDNA clone 23443 3′. W60268_at zd29g01.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 342096 5′. AA465016_at zx80d02.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810051 5′ similar to TR: G1020091 G1020091 NEUROPSIN.; contains element LTR3 repetitive element;. RC_T79842_at yd83f04.s1 Homo sapiens cDNA clone 114847 3′. RC_AA206225_at zq56g08.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA clone 645662 3′. RC_AA449914_at zx37g02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 788690 3′. RC_F10211_at H. sapiens partial cDNA sequence; clone c-3bh08. RC_AA480109_r_(—) zv41f05.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 756225 3′ similar to TR: G498729 G498729 ZINC FINGER PROTEIN;. RC_AA053102_s_(—) zl72a06.s1 Stratagene colon (#937204) Homo sapiens cDNA at clone 510130 3′. RC_AA434113_at zw24b11.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 770205 3′ similar to contains element TAR1 repetitive element;. RC_AA441791_at zw62c02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 774626 3′. RC_N67583_at yz42c02.s1 Homo sapiens cDNA clone 285698 3′. RC_T96077_at ye47b12.s1 Homo sapiens cDNA clone 120863 3′. AB002316_at Human mRNA for KIAA0318 gene, partial cds. RC_W96222_at ze10g07.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 358620 3′. M16591_s_at Human hemopoietic cell protein-tyrosine kinase (HCK) gene. complete cds, clone lambda-a2/1a RC_N59808_at yz76b12.s1 Homo sapiens cDNA clone 288959 3′. RC_F10040_at H. sapiens partial cDNA sequence; clone c-39g09. RC_AA461549_at zx62b09.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 796025 3′. RC_W68683_at zd35d04.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 342631 3′. RC_AA084640_at zn20d05.s1 Stratagene neuroepithelium NT2RAMl 937234 Homo sapiens cDNA clone 547977 3′. C01169_at HUMGS0007858, Human Gene Signature, 3′-directed cDNA sequence. RC_AA491465_at ab04a05.s1 Stratagene fetal retina 937202 Homo sapiens cDNA clone 839792 3′. RC_W67564_s_at zd41c07.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 343212 3′. J03019_s_at Human beta-1-adrenergic receptor mRNA, complete cds. RC_H80622_at yu77b06.s1 Homo sapiens cDNA clone 239795 3′. RC_N34686_at yy15h06.s1 Homo sapiens cDNA clone 271355 3′. RC_R56066_s_at yg91d08.s1 Homo sapiens cDNA clone 40992 3′. RC_T34611_at EST71577 Homo sapiens cDNA 3′ end similar to None. RC_AA031373_s_(—) zk15e12.s1 Soares pregnant uterus NbHPU Homo sapiens at cDNA clone 470638 3′. X52056_at Human mRNA for spi-1 proto-oncogene N77564_at yz89g12.r1 Homo sapiens cDNA clone 290278 5′. C01765_at HUMGS0003713, Human Gene Signature, 3′-directed cDNA sequence. RC_AA496936_at ae32d03.s1 Gessler Wilms tumor Homo sapiens cDNA clone 897509 3′. RC_AA027103_at zk04e03.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 469564 3′. RC_R44131_at yg32c11.s1 Homo sapiens cDNA clone 34089 3′. RC_N67227_at yz48f04.s1 Homo sapiens cDNA clone 286303 3′. RC_T96677_at ye52f03.s1 Homo sapiens cDNA clone 121373 3′. RC_AA134965_i_(—) zo23g05.s1 Stratagene colon (#937204) Homo sapiens cDNA at clone 587768 3′. RC_T86600_at yd87d10.s1 Homo sapiens cDNA clone 115219 3′. RC_AA054087_at zf51f03.s1 Soares retina N2bHR Homo sapiens cDNA clone 380477 3′. AA444374_at zv76b10.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA 5′. RC_H72357_at ys04f01.s1 Homo sapiens cDNA clone 213817 3′ similar to gb: J04970 CARBOXYPEPTIDASE M PRECURSOR (HUMAN); contains Alu repetitive element;. RC_AA017045_at ze37d11.s1 Soares retina N2b4HR Homo sapiens cDNA clone 361173 3′. AA010324_at zi09c03.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 430276 5′. RC_AA234743_at zs38b09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 687449 3′. RC_AA055892_at zf20d06.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 377483 3′. RC_AA446650_at zw89g02.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 784178 3′. H91747_s_at ys80e03.r1 Homo sapiens cDNA clone 221116 5′. AA401510_s_at zu63c08.r1 Soares testis NHT Homo sapiens cDNA clone 742670 5′. RC_W61239_at zd31d10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 342259 3′. or a sequence as identified below expressed in mixed tumors

AA203639_at zx58c10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 446706 5′ similar to contains Alu repetitive element;. M11844_at Human prealbumin gene, complete cds. RC_AA206042_at zq77f02.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA clone 647643 3′ similar to contains element MSR1 repetitive element;. RC_N51097_at yz03e04.s1 Homo sapiens cDNA clone 281982 3′. RC_H05527_at yl70f08.s1 Soares infant brain 1NIB Homo sapiens cDNA clone 43327 3′. AA115572_s_at zl05d11.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491445 5′ similar to TR: G895845 G895845 PUTATIVE P64 CLCP PROTEIN.;. RC_H12863_at yj14b12.s1 Homo sapiens cDNA clone 148703 3′. AA489287_at ab36e04.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842910 5′. RC_T96383_at ye49h07.s1 Homo sapiens cDNA clone 121117 3′. RC_H56453_at yq98g12.s1 Homo sapiens cDNA clone 203878 3′. RC_AA152194_at zl03h01.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491281 3′. RC_Z38520_at H. sapiens partial cDNA sequence; clone c-0ed05. RC_R38944_at yd06g09.s1 Homo sapiens cDNA clone 25061 3′ similar to contains Alu repetitive element;. RC_AA133926_at zo16e11.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 587084 3′. RC_N69908_f_at za68f06.s1 Homo sapiens cDNA clone 297731 3′ similar to gb: X59244 ZINC FINGER PROTEIN 43 (HUMAN);. RC_AA151945_at zo02c02.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 566498 3′ similar to contains Alu repetitive element;. S83308_at SOX5 = Sry-related HMG box gene {alternatively spliced} [human, testis, mRNA, 1473 nt] RC_AA406570_at zv11b06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 753299 3′. RC_AA058314_at zl67g04.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 509718 3′ similar to contains Alu repetitive element; contains element PTR5 repetitive element;. RC_R98735_at yr31g12.s1 Homo sapiens cDNA clone 206950 3′.

The genes selected may be a gene from each gene group being expressed in a significantly lower amount in that stage than in one of the other stages.

Expression Patterns

The objects of the invention are achieved by providing one or more of the embodiments described below. In one embodiment a method is provided for determining an expression pattern of a cell sample preferably independent of the proportion of submucosal, muscle and connective tissue cells present. Expression is determined of one or more genes in a sample comprising cells, said genes being selected from the same genes as discussed above and shown in the tables.

It is an object of the present invention that characteristic patterns of expression of genes can be used to characterize different types of tissue. Thus, for example gene expression patterns can be used to characterize stages and grades of bladder tumors. Similarly, gene expression patterns can be used to distinguish cells having a bladder origin from other cells. Moreover, gene expression of cells which routinely contaminate bladder tumor biopsies has been identified, and such gene expression can be removed or subtracted from patterns obtained from bladder biopsies. Further, the gene expression patterns of single-cell solutions of bladder tumor cells have been found to be substantially without interfering expression of contaminating muscle, submucosal, and connective tissue cells than biopsy samples.

The one or more genes exclude genes which are expressed in the submucosal, muscle, and connective tissue. A pattern of expression is formed for the sample which is independent of the proportion of submucosal, muscle, and connective tissue cells in the sample.

In another aspect of the invention a method of determining an expression pattern of a cell sample is provided. Expression is determined of one or more genes in a sample comprising cells. A first pattern of expression is thereby formed for the sample. Genes which are expressed in submucosal, muscle, and connective tissue cells are removed from the first pattern of expression, forming a second pattern of expression which is independent of the proportion of submucosal, muscle, and connective tissue cells in the sample.

Another embodiment of the invention provides a method for determining an expression pattern of a bladder mucosa or bladder cancer cell. Expression is determined of one or more genes in a sample comprising bladder mucosa or bladder cancer cells; the expression determined forms a first pattern of expression. A second pattern of expression which was formed using the one or more genes and a sample comprising predominantly submucosal, muscle, and connective tissue cells, is subtracted from the first pattern of expression, forming a third pattern of expression. The third pattern of expression reflects expression of the bladder mucosa or bladder cancer cells independent of the proportion of submucosal, muscle, and connective tissue cells present in the sample.

Diagnosing

In another embodiment of the invention a method is provided for detecting an invasive tumor in a patient. A marker is detected in a sample of a body fluid. The body fluid is selected from the group consisting of blood, plasma, serum, faeces, mucus, sputum, cerebrospinal fluid and/or urine. The marker is an mRNA or protein expression product of a gene which is more prevalent in submucosal, muscle, and connective tissue than in the body fluid. An increased amount of the marker in the body fluid indicates a tumor which has become invasive in the patient.

In another aspect of the invention a method is provided for diagnosing a bladder cancer. A first pattern of expression is determined of one or more genes in a sample from bladder tissue suspected of being neoplastic. The first pattern of expression is compared to a second and third reference pattern of expression. The second pattern is of the one or more genes in normal bladder mucosa and the third pattern is of the one or more genes in bladder cancer. A first pattern of expression which is found to be more similar to the third pattern than the second indicates neopiasia of the bladder tissue sample.

According to yet another aspect of the invention a method is provided for predicting the outcome, or prescribing a treatment of a bladder tumor. A first pattern of expression is determined of one or more genes in a bladder tumor sample. The first pattern is compared to one or more reference patterns of expression determined for bladder tumors at a grade between I and IV. The reference pattern which shares maximum similarity with the first pattern is identified. The outcome or treatment appropriate for the grade of tumor of the reference pattern with the maximum similarity is assigned to the bladder tumor sample.

In another embodiment of the invention a method is provided for determining the grade of a bladder tumor. A first pattern of expression is determined of one or more genes in a bladder tumor sample. The first pattern is compared to one or more reference patterns of expression determined for bladder tumors at a grade between I and IV. The grade of the reference pattern with the maximum similarity is assigned to the bladder tumor sample.

Yet another embodiment of the invention provides a method to determine the stage of a bladder tumor as described above. A first pattern of expression is determined of one or more genes in a bladder tumor sample. The first pattern is compared to one or more reference patterns of expression determined for bladder tumors at different stages. The reference pattern which shares maximum similarity with the first pattern is identified. The stage of the reference pattern with the maximum similarity is assigned to the bladder tumor sample.

In still another embodiment of the invention a method is provided for identifying a tissue sample as being from bladder. A first pattern of expression is determined for one or more genes in a tissue sample. The first pattern is compared to a second pattern of expression determined, obtained for normal mucosa cells. Similarities between the first and the second patterns suggest that the tissue sample is mucosa in its origin. This method being particularly useful when diagnosing metastasis possibly distant from its origin.

Another aspect of the invention is a method to aid in diagnosing, predicting the outcome, or prescribing treatment of bladder cancer. A first pattern of expression is determined for one or more genes in a first bladder tissue sample. And a second pattern of expression is determined for the one or more genes in a second bladder tissue sample. The first bladder tissue sample is a normal bladder mucosa sample or an earlier stage or lover grade of bladder tumor than the second bladder tissue sample. The first pattern of expression is compared to the second pattern of expression to identify a first set of genes which are increased in the second bladder tissue sample relative to the first bladder tissue sample, and a second set of genes which are decreased in the second bladder tissue sample relative to the first bladder tissue sample. Those genes which are expressed in submucosal, muscle or connective tissue are removed from the first set of genes. Those genes which are not expressed in submucosal, muscle, or connective tissue are removed from the second set of genes.

Independence of Submucosal, Muscle and Conn Ctive Tissue

Since a biopsy of the tissue often contains more tissue material such as connective tissue than the tissue to be examined, when the tissue to be examined is epithelial or mucosa, the invention also relates to methods, wherein the expression pattern of the tissue is independent of the amount of connective tissue in the sample.

Biopsies contain epithelial cells that most often are the targets for the studies, and in addition many other cells that contaminate the epithelial cell fraction to a varying extent. The contaminants include histiocytes, endothelial cells, leukocytes, nerve cells, muscle cells etc. Micro dissection is the method of choice for DNA examination, but in the case of expression studies this procedure is difficult due to RNA degradation during the procedure. The epithelium may be gently removed and the expression in the remaining submucosa and underlying connective tissue (the bladder wall) monitored. Genes expressed at high or low levels in the bladder wall should be interrogated when performing expression monitoring of the mucosa and tumors. A similar approach could be used for studies of epithelia in other organs.

In one embodiment of the invention normal mucosa lining the bladder lumen from bladders for cancer is scraped off. Then biopsies is taken from the denuded submucosa and connective tissue, reaching approximately 5 mm into the bladder wall, and immediately disintegrated in guanidinium isothiocyanate. Total RNA may be extracted, pooled, and poly(A)⁺ mRNA may be prepared from the pool followed by conversion to double-stranded cDNA and in vitro transcription into cDNA containing biotin-labeled CTP and UTP.

Genes that are expressed and genes that are not expressed in bladder wall can both interfere with the interpretation of the expression in a biopsy, and should be considered when interpreting expression intensities in tumor biopsies, as the bladder wall component of a biopsy varies in amount from biopsy to biopsy.

When having determined the pattern of genes expressed in bladder wall components said pattern may be subtracted from a pattern obtained from the sample resulting in a third pattern related to the mucosa (epithelial) cells.

In another aspect of the invention a method is provided for determining an expression pattern of a bladder tissue sample independent of the proportion of submucosal, muscle and connective tissue cells present. A single-cell suspension of disaggregated bladder tumor cells is isolated from a bladder tissue sample comprising bladder tumor cells is isolated from a bladder tissue sample comprising bladder cells, submucosal cells, muscle cells, and connective tissue cells. A pattern of expression is thus formed for the sample which is independent of the proportion of submucosal, muscle, and connective tissue cells in the bladder tissue sample.

Yet another method relates to the elimination of mRNA from bladder wall components before determining the pattern, e.g. by filtration and/or affinity chromatography to remove mRNA related to the bladder wall.

Detection

Working with human tumor material requires biopsies, and working with RNA requires freshly frozen or immediately processed biopsies, or chemical pretreatment of the biopsy. Apart from the cancer tissue, biopsies do inevitably contain many different cell types, such as cells present in the blood, connective and muscle tissue, endothelium etc. In the case of DNA studies, microdissection or laser capture are methods of choice, however the time-dependent degradation of RNA makes it difficult to perform manipulation of the tissue for more than a few minutes. Furthermore, studies of expressed sequences may be difficult on the few cells obtained via microdissection or laser capture, as these cells may have an expression pattern that deviates from the predominant pattern in a tumor due to large intratumoral heterogeneity.

In the present context high density expression arrays may be used to evaluate the impact of bladder wall components in bladder tumor biopsies, and tested preparation of single cell solutions as a means of eliminating the contaminants. The results of these evaluations permit for the design of methods of evaluating bladder samples without the interfering background noise caused by ubiquitous contaminating submucosal, muscle, and connective tissue cells. The evaluating assays of the invention may be of any type.

While high density expression arrays can be used, other techniques are also contemplated. These include other techniques for assaying for specific mRNA species, including RT-PCR and Northern Blotting, as well as techniques for assaying for particular protein products, such as ELISA, Western blotting, and enzyme assays. Gene expression patterns according to the present invention are determined by measuring any gene product of a particular gene, including mRNA and protein. A pattern may be for one or more genes.

RNA or protein can be isolated and assayed from a test sample using any techniques known in the art. They can for example be isolated from a fresh or frozen biopsy, from formalin-fixed tissue, from body fluids, such as blood, plasma, serum, urine, or sputum.

Detection of Expression

Expression of genes may in general be detected by either detecting mRNA from the cells and/or detecting expression products, such as peptides and proteins.

mRNA Detection

The detection of mRNA of the invention may be a tool for determining the developmental stage of a cell type which may be definable by its pattern of expression of messenger RNA. For example, in particular stages of cells, high levels of ribosomal RNA are found whereas relatively low levels of other types of messenger RNAs may be found. Where a pattern is shown to be characteristic of a stage, said stage may be defined by that particular pattern of messenger RNA expression. The mRNA population is a good determinant of a developmental stage, and maybe correlated with other structural features of the cell. In this manner, cells at specific developmental stages will be characterized by the intracellular environment, as well as the extracellular environment. The present invention also allows the combination of definitions based in part upon antigens and in part upon mRNA expression. In one embodiment, the two may be combined in a single incubation step. A particular incubation condition may be found which is compatible with both hybridization recognition and non-hybridization recognition molecules. Thus, e.g. an incubation condition may be selected which allows both specificity of antibody binding and specificity of nucleic acid hybridization. This allows simultaneous performance of both types of interactions on a single matrix. Again, where developmental mRNA patterns are correlated with structural features, or with probes which are able to hybridize to intracellular mRNA populations, a cell sorter may be used to sort specifically those cells having desired mRNA population patterns.

It is within the general scope of the present invention to provide methods for the detection of mRNA. Such methods often involve sample extraction, PCR amplification, nucleic acid fragmentation and labeling, extension reactions, and transcription reactions.

Sample Preparation

The nucleic acid (either genomic DNA or mRNA) may be isolated from the sample according to any of a number of methods well known to those of skill in the art. One of skill will appreciate that where alterations in the copy number of a gene are to be detected genomic DNA is preferably isolated. Conversely; where expression levels of a gene or genes are to be detected, preferably RNA (mRNA) is isolated.

Methods of isolating total mRNA are well known to those of skill in the art. In one embodiment, the total nucleic acid is isolated from a given sample using, for example, an acid guanidinium-phenol-chloroform extraction method and polyA.sup. and mRNA is isolated by oligo dT column chromatography or by using (dT)n magnetic beads (see, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (2nd.ed.), Vols. 1-3, Cold Spring Harbor Laboratory, (1989), or Current Protocols in Molecular Biology, F. Ausubel et al., ed. Greene Publishing and Wiley-Interscience, New York (1987)).

The sample may be from tissue and/or body fluids, as defined elsewhere herein. Before analyzing the sample, e.g., on an oligonucleotide array, it will often be desirable to perform one or more sample preparation operations upon the sample. Typically, these sample preparation operations will include such manipulations as extraction of intracellular material, e.g., nucleic acids from whole cell samples, viruses, amplification of nucleic acids, fragmentation, transcription, labeling and/or extension reactions. One or more of these various operations may be readily incorporated into the device of the present invention.

DNA Extraction

DNA extraction may be relevant under circumstances where possible mutations in the genes are to be determined in addition to the determination of expression of the genes.

For those embodiments where whole cells, or other tissue samples are being analyzed, it will typically be necessary to extract the nucleic acids from the cells or viruses, prior to continuing with the various sample preparation operations. Accordingly, following sample collection, nucleic acids may be liberated from the collected cells, viral coat etc. into a crude extract followed by additional treatments to prepare the sample for subsequent operations, such as denaturation of contaminating (DNA binding) proteins, purification, filtration and desalting.

Liberation of nucleic acids from the sample cells, and denaturation of DNA binding proteins may generally be performed by physical or chemical methods. For example, chemical methods generally employ lysing agents to disrupt the cells and extract the nucleic acids from the cells, followed by treatment of the extract with chaotropic salts such as guanidinium isothiocyanate or urea to denature any contaminating and potentially interfering proteins.

Alternatively, physical methods may be used to extract the nucleic acids and denature DNA binding proteins, such as physical protrusions within microchannels or sharp edged particles piercing cell membranes and extract their contents. Combinations of such structures with piezoelectric elements for agitation can provide suitable shear forces for lysis.

More traditional methods of cell extraction may also be used, e.g., employing a channel with restricted cross-sectional dimension which causes cell lysis when the sample is passed through the channel with sufficient flow pressure. Alternatively, cell extraction and denaturing of contaminating proteins may be carried out by applying an alternating electrical current to the sample. More specifically, the sample of cells is flowed through a microtubular array while an alternating electric current is applied across the fluid flow. Subjecting cells to ultrasonic agitation, or forcing cells through microgeometry apertures, thereby subjecting the cells to high shear stress resulting in rupture are also possible extraction methods.

Filtration

Following extraction, it will often be desirable to separate the nucleic acids from other elements of the crude extract, e.g. denatured proteins, cell membrane particles and salts. Removal of particulate matter is generally, accomplished by filtration or flocculation. Further, where chemical denaturing methods are used, it may be desirable to desalt the sample prior to proceeding to the next step. Desalting of the sample and isolation of the nucleic acid may generally be carried out in a single step, e.g. by binding the nucleic acids to a solid phase and washing away the contaminating salts, or performing gel filtration chromatography on the sample passing salts through dialysis membranes. Suitable solid supports for nucleic acid binding include e.g. diatomaceous earth or silica (i.e., glass wool). Suitable gel exclusion media also well known in the art may be readily incorporated into the devices of the present invention and is commercially available from, e.g., Pharmacia and Sigma Chemical.

Alternatively, desalting methods may generally take advantage of the high electrophoretic mobility and negativity of DNA compared to other elements.

Electrophoretic methods may also be utilized in the purification of nucleic acids from other cell contaminants and debris. Upon application of an appropriate electric field, the nucleic acids present in, the sample will migrate toward the positive electrode and become trapped on the capture membrane. Sample impurities remaining free of the membrane are then washed away by applying an appropriate fluid flow. Upon reversal of the voltage, the nucleic acids are released from the membrane in a substantially purer form. Further, coarse filters may also be overlaid on the barriers to avoid any fouling of the barriers by particulate matter, proteins or nucleic acids, thereby permitting repeated use.

Separation of Contaminants by Chromatography

In a similar aspect, the high electrophoretic mobility of nucleic acids with their negative charges, may be utilized to separate nucleic acids from contaminants by utilizing a short column of a gel or other appropriate matrices or gels which will slow or retard the flow of other contaminants while allowing the faster nucleic acids to pass.

This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said oligonucleotides is greater than about 60 different oligonucleotides per 1 cm.sup.2, and all of said different oligonucleotides have an identical terminal 3′ nucleic acid sequence and an identical terminal 5′ nucleic acid sequence b) amplifying said multiplicity of oligonucleotides to provide a pool of amplified nucleic acids; and c) attaching the pool of nucleic acids to a solid support.

For example, nucleic acid affinity chromatography is based on the tendency of complementary, single-stranded nucleic acids to form a double-stranded or duplex structure through complementary base pairing. A nucleic acid (either DNA or RNA) can easily be attached to a solid substrate (matrix) where it acts as an immobilized ligand that interacts with and forms duplexes with complementary nucleic acids present in a solution contacted to the immobilized ligand. Unbound components can be washed away from the bound complex to either provide a solution lacking the target molecules bound to the affinity column, or to provide the isolated target molecules themselves. The nucleic acids captured in a hybrid duplex can be separated and released from the affinity matrix by denaturation either through heat, adjustment of salt concentration, or the use of a destabilizing agent such as formamide, TWEEN.TM.-20 denaturing agent, or sodium dodecyl sulfate (SDS).

Affinity columns (matrices) are typically used either to isolate a single nucleic acid typically by providing a single species of affinity ligand. Alternatively, affinity columns bearing a single affinity ligand (e.g. oligo dt columns) have been used to isolate a multiplicity of nucleic acids where the nucleic acids all share a common sequence (e.g. a polyA).

Affinity Matrices

The type of affinity matrix used depends on the purpose of the analysis. For example, where it is desired to analyze mRNA expression levels of particular genes in a complex nucleic acid sample (e.g., total mRNA) it is often desirable to eliminate nucleic acids produced by genes that are constitutively overexpressed and thereby tend to mask gene products expressed at characteristically lower levels. Thus, in one embodiment, the affinity matrix can be used to remove a number of preselected gene products (e.g., actin, GAPDH, etc.). This is accomplished by providing an affinity matrix bearing nucleic acid affinity ligands complementary to the gene products (e.g., mRNAs or nucleic acids derived therefrom) or to subsequences thereof. Hybridization of the nucleic acid sample to the affinity matrix will result in duplex formation between the affinity ligands and their target nucleic acids. Upon elution of the sample from the affinity matrix, the matrix will retain the duplexes nucleic acids leaving a sample depleted of the overexpressed target nucleic acids.

The affinity matrix can also be used to identify unknown mRNAs or cDNAs in a sample. Where the affinity matrix contains nucleic acids complementary to every known gene (e.g., in a cDNA library, DNA reverse transcribed from an mRNA, mRNA used directly or amplified, or polymerized from a DNA template) in a sample, capture of the known nucleic acids by the affinity matrix leaves a sample enriched for those nucleic acid sequences that are unknown. In effect, the affinity matrix is used to perform a subtractive hybridization to isolate unknown nucleic acid sequences. The remaining “unknown” sequences can then be purified and sequenced according to standard methods.

The affinity matrix can also be used to capture (isolate) and thereby purify unknown nucleic acid sequences. For example, an affinity matrix can be prepared that contains nucleic acid. (affinity ligands) that are complementary to sequences not previously identified, or not previously known to be expressed in a particular nucleic acid sample. The sample is then hybridized to the affinity matrix and those sequences that are retained on the affinity matrix are “unknown” nucleic acids. The retained nucleic acids can be eluted from the matrix (e.g. at increased temperature, increased destabilizing agent concentration, or decreased salt) and the nucleic acids can then be sequenced according to standard methods.

Similarly, the affinity matrix can be used to efficiently capture (isolate) a number of known nucleic acid sequences. Again, the matrix is prepared bearing nucleic acids complementary to those nucleic acids it is desired to isolate. The sample is contacted to the matrix under conditions where the complementary nucleic acid sequences hybridize to the affinity ligands in the matrix. The non-hybridized material is washed off the matrix leaving the desired sequences bound. The hybrid duplexes are then denatured providing a pool of the isolated nucleic acids. The different nucleic acids in the pool can be subsequently separated according to standard methods (e.g. gel electrophoresis).

As indicated above the affinity matrices can be used to selectively remove nucleic acids from virtually any sample containing nucleic acids (e.g. in a cDNA library, DNA reverse transcribed from an mRNA, mRNA used directly or amplified, or polymerized from a DNA template, and so forth). The nucleic acids adhering to the column can be removed by washing with a low salt concentration buffer, a buffer containing a destabilizing agent such as formamide, or by elevating the column temperature.

In one particularly preferred embodiment, the affinity matrix can be used in a method to enrich a sample for unknown RNA sequences (e.g. expressed sequence tags (ESTs)). The method involves first providing an affinity matrix bearing a library of oligonucleotide probes specific to known RNA (e.g., EST) sequences. Then, RNA from undifferentiated and/or unactivated cells and RNA from differentiated or activated or pathological, (e.g., transformed) or otherwise having a different metabolic state are separately hybridized against the affinity matrices to provide two pools of RNAs lacking the known RNA sequences.

In a preferred embodiment, the affinity matrix is packed into a columnar casing. The sample is then applied to the affinity matrix (e.g. injected onto a column or applied to a column by a pump such as a sampling pump driven by an autosampler). The affinity matrix (e.g. affinity column) bearing the sample is subjected to conditions under which the nucleic acid probes comprising the affinity matrix hybridize specifically with complementary target nucleic acids. Such conditions are accomplished by maintaining appropriate pH, salt and temperature conditions to facilitate hybridization as discussed above.

For a number of applications, it may be desirable to extract and separate messenger RNA from cells, cellular debris, and other contaminants. As such, the device of the present invention may, in some cases, include a mRNA purification chamber or channel. In general, such purification takes advantage of the poly-A tails on mRNA. In particular and as noted above, poly-T oligonucleotides may be immobilized within a chamber or channel of the device to serve as affinity ligands for mRNA. Poly-T oligonucleotides may be immobilized upon a solid support incorporated within the chamber or channel, or alternatively, may be immobilized upon the surface(s) of the chamber or channel itself. Immobilization of oligonucleotides on the surface of the chambers or channels may be carried out by methods described herein including, e.g., oxidation and silanation of the surface followed by standard DMT synthesis of the oligonucleotides.

In operation, the lysed sample is introduced to a high salt solution to increase the ionic strength for hybridization, whereupon the mRNA will hybridize to the immobilized poly-T. The mRNA bound to the immobilized poly-T oligonucleotides is then washed free in a low ionic strength buffer. The poly-T oligonucleotides may be immobiliized upon poroussurfaces, e.g., porous silicon, zeolites silica xerogels, scintered particles, or other solid supports.

Hybridization

Following sample preparation, the sample can be subjected to one or more different analysis operations. A variety of analysis operations may generally be performed, including size based analysis using, e.g., microcapillary electrophoresis, and/or sequence based analysis using, e.g., hybridization to an oligonucleotide array.

In the latter case, the nucleic acid sample may be probed using an array of oligonucleotide probes. Oligonucleotide arrays generally include a substrate having a large number of positionally distinct oligonucleotide probes attached to the substrate. These arrays may be produced using mechanical or light directed synthesis methods which incorporate a combination of photolithographic methods and solid phase oligonucleotide synthesis methods.

Light Directed Synthesis of Oligonucleotide Arrays

The basic strategy for light directed synthesis of oligonucleotide arrays is as follows. The surface of a solid support, modified with photosensitive protecting groups is illuminated through a photolithographic mask, yielding reactive hydroxyl groups in the illuminated regions. A selected nucleotide, typically in the form of a 3′-O-phosphoramidite-activated deoxynucleoside (protected at the 5′ hydroxyl with a photosensitive protecting group), is then presented to the surface and coupling occurs at the sites that were exposed to light. Following capping and oxidation, the substrate is rinsed and the surface is illuminated through a second mask to expose additional hydroxyl groups for coupling. A second selected nucleotide (e.g., 5′-protected, 3′-O-phosphoramidite-activated deoxynucleoside) is presented to the surface. The selective deprotection and coupling cycles are repeated until the desired set of products is obtained. Since photolithography is used the process can be readily miniaturized to generate high density arrays of oligonucleotide probes. Furthermore, the sequence of the oligonucleotides at each site is known. See Pease et al. Mechanical synthesis methods are similar to the light directed methods except involving mechanical direction of fluids for deprotection and addition in the synthesis steps.

For some embodiments, oligonucleotide arrays may be prepared having all possible probes of a given length. The hybridization pattern of the target sequence on the array may be used to reconstruct the target DNA sequence. Hybridization analysis of large numbers of probes can be used to sequence long stretches of DNA or provide an oligonucleotide array which is specific and complementary to a particular nucleic acid sequence. For example, in particularly preferred aspects, the oligonucleotide array will contain oligonucleotide probes which are complementary to specific target sequences, and individual or multiple mutations of these. Such arrays are particularly useful in the diagnosis of specific disorders which are characterized by the presence of a particular nucleic acid sequence.

Following sample collection and nucleic acid extraction, the nucleic acid portion of the sample is typically subjected to one or more preparative reactions. These preparative reactions include in vitro transcription, labeling, fragmentation, amplification and other reactions. Nucleic acid amplification increases the number of copies of the target nucleic acid sequence of interest. A variety of amplification methods are suitable for use in the methods and device of the present invention, including for example, the polymerase chain reaction method or (PCR), the ligase chain reaction (LCR), self sustained sequence replication (3SR), and nucleic acid based sequence amplification (NASBA).

The latter two amplification methods involve isothermal reactions based on isothermal transcription, which produce both single stranded RNA (ssRNA) and double stranded DNA (dsDNA) as the amplification products in a ratio of approximately 30 or 100 to 1, respectively. As a result, where these latter methods are employed, sequence analysis may be carried out using either type of substrate, i.e. complementary to either DNA or RNA.

Frequently, it is desirable to amplify the nucleic acid sample prior to hybridization. One of skill in the art will appreciate that whatever amplification method is used, if a quantitative result is desired, care must be taken to use a method that maintains or controls for the relative frequencies of the amplified nucleic acids.

PCR

Methods of “quantitative” amplification are well known to those of skill in the art. For example, quantitative PCR involves simultaneously co-amplifying a known quantity of a control sequence using the same primers. This provides an internal standard that may be used to calibrate the PCR reaction. The high density array may then include probes specific to the internal standard for quantification of the amplified nucleic acid.

Thus, in one embodiment, this invention provides-for a method of optimizing a probe set for detection of a particular gene. Generally, this method involves providing a high density array containing a multiplicity of probes of one or more particular length(s) that are complementary to subsequences of the mRNA transcribed by the target gene. In one embodiment the high density array may contain every probe of a particular length that is complementary to a particular mRNA. The probes of the high density array are then hybridized with their target nucleic acid alone and then hybridized with a high complexity, high concentration nucleic acid sample that does not contain the targets complementary to the probes. Thus, for example, where the target nucleic acid is an RNA, the probes are first hybridized with their target nucleic acid alone and then hybridized with RNA made from a cDNA library (e.g., reverse transcribed polyA.sup.+mRNA) where the sense of the hybridized RNA is opposite that of the target nucleic acid (to insure that the high complexity sample does not contain targets for the probes). Those probes that show a strong hybridization signal with their target and little or no cross-hybridization with the high complexity sample are preferred probes for use in the high density arrays of this invention.

PCR amplification generally involves the use of one strand of the target nucleic acid sequence as a template for producing a large number of complements to that sequence. Generally, two primer sequences complementary to different ends of a segment of the complementary strands of the target sequence hybridize with their respective strands of the target sequence, and in the presence of polymerase enzymes and nucleoside triphosphates, the primers are extended along the target sequence. The extensions are melted from the target sequence and the process is repeated, this time with the additional copies of the target sequence synthesized in the preceding steps. PCR amplification typically involves repeated cycles of denaturation, hybridization and extension reactions to produce sufficient amounts of the target nucleic acid. The first step of each cycle of the PCR involves the separation of the nucleic acid duplex formed by the primer extension. Once the strands are separated, the next step in PCR involves hybridizing the separated strands with primers that flank the target sequence. The primers are then extended to form complementary copies of the target strands. For successful PCR amplification, the primers are designed so that the position at which each primer hybridizes along a duplex sequence is such that an extension product synthesized from one primer, when separated from the template (complement), serves as a template for the extension of the other primer. The cycle of denaturation, hybridization, and extension is repeated as many times as necessary to obtain the desired amount of amplified nucleic acid.

In PCR methods, strand separation is normally achieved by heating the reaction to a sufficiently high temperature for a sufficient time to cause the denaturation of the duplex but not to cause an irreversible denaturation of the polymerase. Typical heat denaturation involves temperatures ranging from about 80.degree. C. to 105.degree. C. for times ranging from seconds to minutes. Strand separation, however, can be accomplished by any suitable denaturing method including physical, chemical, or enzymatic means. Strand separation may be induced by a helicase, for example, or an enzyme capable of exhibiting helicase activity.

In addition to PCR and IVT reactions, the methods and devices of the present invention are also applicable to a number of other reaction types, e.g., reverse transcription, nick translation, and the like.

Labelling Before Hybridization

The nucleic acids in a sample will generally be labeled to facilitate detection in subsequent steps. Labeling may be carried out during the amplification, in vitro transcription or nick translation processes. In particular, amplification, in vitro transcription or nick translation may incorporate a label into the amplified or transcribed sequence, either through the use of labeled primers or the incorporation of labeled dNTPs into the amplified sequence.

Hybridization between the sample nucleic acid and the oligonucleotide probes upon the array is then detected, using, e.g., epifluorescence confocal microscopy. Typically, sample is mixed during hybridization to enhance hybridization of nucleic acids in the sample to nucleoc acid probes on the array.

Labelling After Hybridization

In some cases, hybridized oligonucleotides may be labeled following hybridization. For example, where biotin labeled dNTPs are used in, e.g. amplification or transcription, streptavidin linked-reporter groups may be used to label hybridized complexes. Such operations are readily integratable into the systems of the present invention. Alternatively, the nucleic acids in the sample may be labeled following amplification. Post amplification labeling typically involves the covalent, attachment of a particular detectable group upon the amplified sequences. Suitable labels or detectable groups include a variety of fluorescent or radioactive labeling groups well known in the art. These labels may also be coupled to the sequences using methods that are well known in the art.

Methods for detection depend upon the label selected. A fluorescent label is preferred because of its extreme sensitivity and simplicity. Standard labeling procedures are used to determine the positions where interactions between a sequence and a reagent take place. For example, if a target sequence is labeled and exposed to a matrix of different probes, only those locations where probes do interact with the target will exhibit any signal. Alternatively, other methods may be used to scan the matrix to determine where interaction takes place. Of course, the spectrum of interactions may be determined in a temporal manner by repeated scans of interactions which occur at each of a multiplicity of conditions. However, instead of testing each individual interaction separately, a multiplicity of sequence interactions may be simultaneously determined on a matrix.

Means of detecting labeled target (sample) nucleic acids hybridized to the probes of the high density array are known to those of skill in the art. Thus, for example, where a colorimetric label is used, simple visualization of the label is sufficient. Where a radioactive labeled probe is used, detection of the radiation (e.g with photographic film or a solid state detector) is sufficient.

In a preferred embodiment, however, the target nucleic acids are labeled with a fluorescent label and the localization of the label on the probe array is accomplished with fluorescent microscopy. The hybridized array is excited with a light source at the excitation wavelength of the particular fluorescent label and the resulting fluorescence at the emission wavelength is detected. In a particularly preferred embodiment, the excitation light source is a laser appropriate for the excitation of the fluorescent label.

The target polynucleotide may be labeled by any of a number of convenient detectable markers. A fluorescent label is preferred because it provides a very strong signal with low background. It is also optically detectable at high resolution and sensitivity through a quick scanning procedure. Other potential labeling moieties include, radioisotopes, chemiluminescent compounds, labeled, binding proteins, heavy metal atoms, spectroscopic markers, magnetic labels, and linked enzymes. Another method for labeling may bypass any label of the target sequence. The target may be exposed to the probes, and a double strand hybrid is formed at those positions only. Addition of a double strand specific reagent will detect where hybridization takes place. An intercalative dye such as ethidium bromide may be used as long as the probes themselves do not fold back on themselves to a significant extent forming hairpin loops. However, the length of the hairpin loops in short oligonucleotide probes would typically be insufficient to form a stable duplex.

Suitable chromogens will include molecules and compounds which absorb light in a distinctive range of wavelengths so that a color may be observed, or emit light when irradiated with radiation of a particular wave length or wave length range, e.g., fluorescers. Biliproteins, e.g., phycoerythrin, may also serve as labels.

A wide variety of suitable dyes are available, being primarily chosen to provide an intense color with minimal absorption by their surroundings. Illustrative dye types include quinoline dyes, triarylmethane dyes, acridine dyes, alizarine dyes, phthaleins, insect dyes, azo dyes, anthraquinoid dyes, cyanine dyes, phenazathionium dyes, and phenazoxonium dyes.

A wide variety of fluorescers may be employed either by themselves or in conjunction with quencher molecules. Fluorescers of interest fall into a variety of categories having certain primary functionalities. These primary functionalities include 1- and 2-aminonaphthalene, p,p′-diaminostilbenes, pyrenes, quaternary phenanthridine salts, 9-aminoacridines, p,p′-diaminobenzophenone imines, anthracenes, oxacarbocyanine, merocyanine, 3-aminoequilenin, perylene, bis-benzoxazole, bis-p-oxazolyl benzene, 1,2-benzophenazin, retinol, bis-3-aminopyridinium salts, hellebrigenin, tetracycline, sterophenol, benzimidzaolylphenylamine, 2-oxo-3-chromen, indole, xanthen, 7-hydroxycoumarin, phenoxazine, salicylate, strophanthidin, porphyrins, triarylmethanes and flavin. Individual fluorescent compounds which have functionalities for linking or which can be modified to incorporate such functionalities include, e.g., dansyl chloride; fluoresceins such as 3,6-dihydroxy-9-phenylxanthhydrol; rhodamineisothiocyanate; N-phenyl 1-amino-8-sulfonatonaphthalene; N-phenyl 2-amino-6-sulfonatonaphthalene; 0.4-acetamido-4-isothiocyanato-stilbene-2,2′-disulfonic acid; pyrene-3-sulfonic acid; 2-toluidinonaphthalene-6-sulfonate; N-phenyl, N-methyl 2-aminoaphthalene-6-sulfonate; ethidium bromide; stebrine; auromine-0,2-(9′-anthroyl)palmitate; dansyl phosphatidylethanolamine; N,N′-dioctadecyl oxacarbocyanine; N,N′-dihexyl oxacarbocyanine; merocyanine, 4-(3′-pyrenyl)butyrate; d-3-aminodesoxy-equilenin; 1,2-(9′-anthroyl)stearate; 2-methylanthracene; 9-vinylanthracene; 2,2′-(vinylene-p-phenylene)bisbenzoxazole; p-bis)2-(4-methyl-5-phenyl-oxazolyl) benzene; 6-dimethylamino-1,2-benzophenazin; retinol; bis(3′-aminopyridinium) 1,10-decandiyl diiodide; sulfonaphthylhydrazone of hellibrienin; chlorotetracycline; N-(7-dimethylamino-4-methyl-2-oxo-3-chromenyl)maleimide; N-)p-(2-benzimidazolyl)-phenyl!maleimide; N-(4-fluoranthyl)maleimide; bis(homovanillic acid); resazarin; 4-chloro-7-nitro-2,1,3-benzooxadiazole; merocyanine 540; resorufin; rose bengal; and 2,4-diphenyl-3(2H)-furanone.

Desirably, fluorescers should absorb light above about 300 nm, preferably about 350 nm, and more preferably above about 400 nm, usually emitting at wavelengths greater than about 10 nm higher than the wavelength of the light absorbed. It should be noted that the absorption and emission characteristics of the bound dye may differ from the unbound dye; Therefore, when referring to the various wavelength ranges and characteristics of the dyes, it is intended to indicate the dyes as employed and not the dye which is unconjugated and characterized in an arbitrary solvent.

Fluorescers are generally preferred because by irradiating a fluorescer with light, one can obtain a plurality of emissions. Thus, a single label can provide for a plurality of measurable events.

Detectable signal may also be provided by chemiluminescent and bioluminescent sources. Chemiluminescent sources include a compound which becomes electronically excited by a chemical reaction and may then emit light which serves as the detectible signal or donates energy to a fluorescent acceptor. A diverse number of families of compounds have been found to provide chemiluminescence under a variety of conditions. One family of compounds is 2,3-dihydro-1,-4-phthalazinedione. The most popular compound is luminol, which is the 5-amino compound. Other members of the family include the 5-amino-6,7,8-trimethoxy- and the dimethylamino<calbenz analog. These compounds can be made to luminesce with alkaline hydrogen peroxide or calcium hypochlorite and base. Another family of compounds is the 2,4,5-triphenylimidazoles, with lophine as the common name for the parent product. Chemiluminescent analogs include para-dimethylamino and—methoxy substituents. Chemiluminescence may also be obtained with oxalates, usually oxalyl active esters, e.g., p-nitrophenyl and a peroxide, e.g., hydrogen peroxide, under basic conditions. Alternatively, luciferins may be used in conjunction with luciferase or lucigenins to provide bioluminescence.

Spin labels are provided by reporter molecules with an unpaired electron spin which can be detected by electron spin resonance (ESR) spectroscopy. Exemplary spin labels include organic free radicals, transitional metal complexes, particularly vanadium, copper, iron, and manganese, and the like. Exemplary spin labels include nitroxide free radicals.

Fragmentation

In addition, amplified sequences may be subjected to other post amplification treatments. For example, in some cases, it may be desirable to fragment the sequence prior to hybridization with an oligonucleotide array, in order to provide segments which are more readily accessible to the probes, which avoid looping and/or hybridization to multiple probes. Fragmentation of the nucleic acids may generally be carried out by physical, chemical or enzymatic methods that are known in the art.

Sample Analysis

Following the various sample preparation operations, the sample will generally be subjected to one or more analysis operations. Particularly preferred analysis operations include, e.g. sequence based analyses using an oligonucleotide array and/or size based analyses using, e.g. microcapillary array electrophoresis.

Capillary Electrophoresis

In some embodiments it may be desirable to provide an additional, or alternative means for analyzing the nucleic acids from the sample

Microcapillary array electrophoresis generally involves the use of a thin capillary or channel which may, or may not be filled with a particular separation medium. Electrophoresis of a sample through the capillary provides a size based separation profile for the sample. Microcapillary array electrophoresis generally provides a rapid method for size based sequencing, PCR product analysis and restriction fragment sizing. The high surface to volume ratio of these capillaries allows for the application of higher electric fields across the capillary without substantial thermal variation across the capillary, consequently allowing for more rapid separations. Furthermore, when combined with confocal imaging methods these methods provide sensitivity in the range of attomoles, which is comparable to the sensitivity of radioactive sequencing methods.

In many capillary electrophoresis methods, the capillaries e.g. fused silica capillaries or channels etched, machined or molded into planar substrates, are filled with an appropriate separation/sieving matrix. Typically, a variety of sieving matrices are known in the art may be used in the microcapillary arrays. Examples of such matrices include, e.g. hydroxyethyl cellulose, polyacrylamide and agarose. Gel matrices may be introduced and polymerized within the capillary channel. However, in some cases this may result in entrapment of bubbles within the channels which can interfere with sample separations. Accordingly, it is often desirable to place a preformed separation matrix within the capillary channel(s), prior to mating the planar elements of the capillary portion. Fixing the two parts, e.g. through sonic welding, permanently fixes the matrix within the channel. Polymerization outside of the channels helps to ensure that no bubbles are formed. Further, the pressure of the welding process helps to ensure a void-free system.

In addition to its use in nucleic acid “fingerprinting” and other sized based analyses the capillary arrays may also be used in sequencing applications. In particular, gel based sequencing techniques may be readily adapted for capillary array electrophoresis.

Expression Products

In addition to detection of mRNA or as the sole detection method expression products from the genes discussed above may be detected as indications of the biological condition of the tissue. Expression products may be detected in either the tissue sample as such, or in a body fluid sample, such as blood, serum, plasma, faeces, mucus, sputum, cerebrospinal fluid, and/or urine of the individual.

The expression products, peptides and proteins, may be detected by any suitable technique known to the person skilled in the art.

In a preferred embodiment the expression products are detected by means of specific antibodies directed to the various expression products, such as immunofluorescent and/or immunohistochemical staining of the tissue.

Immunohistochemical localization of expressed proteins may be carried out by immunostaining of tissue sections from the single tumors to determine which cells expressed the protein encoded by the transcript in question. The transcript levels may be used to select a group of proteins supposed to show variation from sample to sample making a rough correlation between the level of protein detected and the intensity of the transcript on the microarray possible.

For example sections may be cut from paraffin-embedded tissue blocks, mounted, and deparaffinized by incubation at 80 C° for 10 min. followed by immersion in heated oil at 60° C. for 10 min. (Estisol 312, Estichem A/Si Denmark) and rehydration. Antigen retrieval is achieved in TEG (TrisEDTA-Glycerol) buffer using microwaves at 900 W. The tissue sections may be cooled in the buffer for 15 min before a brief rinse in tap water. Endogenous peroxidase activity is blocked by incubating the sections with 1% H2O2 for 20 min. followed by three rinses in tap water, 1 min each. The sections may then be soaked in PBS buffer for 2 min. The next steps can be modified from the descriptions given by Oncogene Science Inc., in the Mouse Immunohistochemistry Detection System, XHCO1 (UniTect, Uniondale, N.Y., USA). Briefly, the tissue sections are incubated overnight at 4° C. with primary antibody (against beta-2 microglobulin (Dako), cytokeratin 8, cystatin-C (both from Europa, US), junB, CD59, E-cadherin, apo-E, cathepsin E, vimentin, IGFII (all from Santa Cruz), followed by three rinses in PBS buffer for 5 min each. Afterwards, the sections are incubated with biotinylated secondary antibody for 30 min, rinsed three times with PBS buffer and subsequently incubated with ABC (avidin-biotinlylated horseradish peroxidase complex) for 30 min. followed by three rinses in PBS buffer.

Staining may be performed by incubation with AEC (3-amino-ethylcarbazole) for 10 min. The tissue sections are counter stained with Mayers hematoxylin, washed in tap water for 5 min. and mounted with glycerol-gelatin. Positive and negative controls may be included in each staining round with all antibodies.

In yet another embodiment the expression products may be detected by means of conventional enzyme assays, such as ELISA methods.

Furthermore, the expression products may be detected by means of peptide/protein chips capable of specifically binding the peptides and/or proteins assessed. Thereby an expression pattern may be obtained.

Assay

Thus, in a further aspect the invention relates to an assay for determining an expression pattern of a bladder cell, comprising at least a first marker and/or a second marker, wherein the first marker is capable of detecting a gene from a first gene group as defined above, and/or the second marker is capable of detecting a gene from a second gene group as defined above, correlating the first expression level and/or the second expression level to a standard level of the assessed genes to determine the presence or absence of a biological condition in the animal tissue. The marker(s) are preferably specifically detecting a gene as identified herein.

In another embodiment the assay comprises at least two markers for each gene group.

As discussed above the marker may be any nucleotide probe, such as a DNA, RNA, PNA, or LNA probe capable of hybridising to mRNA indicative of the expression level. The hybridisation conditions are preferably as described below for probes. In another embodiment the marker is an antibody capable of specifically binding the expression product in question.

Detection

Patterns can be compared manually by a person or by a computer or other machine. An algorithm can be used to detect similarities and differences. The algorithm may score and compare, for example, the genes which are expressed and the genes which are not expressed. Alternatively, the algorithm may look for changes in intensity of expression of a particular gene and score changes in intensity between two samples. Similarities may be determined on the basis of genes which are expressed in both samples and genes which are not expressed in both samples or on the basis of genes whose intensity of expression are numerically similar.

Generally, the detection operation will be performed using a reader device external to the diagnostic device. However, it may be desirable in some cases to incorporate the data gathering operation into the diagnostic device itself.

The detection apparatus may be a fluorescence detector, or a spectroscopic detector, or another detector.

Although hybridization is one type of specific interaction which is clearly useful for use in this mapping embodiment antibody reagents may also be very useful.

Data Gathering and Analysis

Gathering data from the various analysis operations, e.g. oligonucleotide and/or microcapillary arrays will typically be carried out using methods known in the art. For example, the arrays may be scanned using lasers to excite fluorescently labeled targets that have hybridized to regions of probe arrays mentioned above, which can then be imaged using charged coupled devices (“CCDs”) for a wide field scanning of the array. Alternatively, another particularly useful method for gathering data from the arrays is through the use of laser confocal microscopy which combines the ease and speed of a readily automated process with high resolution detection.

Following the data gathering operation, the data will typically be reported to a data analysis operation. To facilitate the sample analysis operation, the data obtained by the reader from the device will typically be analyzed using a digital computer. Typically, the computer will be appropriately programmed for receipt and storage of the data from the device, as well as for analysis and reporting of the data gathered, i.e., interpreting fluorescence data to determine the sequence of hybridizing probes, normalization of background and single base mismatch hybridizations, ordering of sequence data in SBH applications, and the like.

It is an object of the present invention to provide a biological sample which may be classified or characterized by analyzing the pattern of specific interactions mentioned above. This may be applicable to a cell or tissue type, to the messenger RNA population expressed by a cell to the genetic content of a cell, or to virtually any sample which can be classified and/or identified by its combination of specific molecular properties.

Pharmaceutical Composition

The invention also relates to a pharmaceutical composition for treating a biological condition, such as bladder tumors.

In one embodiment the pharmaceutical composition comprises one or more of the peptides being expression products as defined above. In a preferred embodiment, the peptides are bound to carriers. The peptides may suitably be coupled to a polymer carrier, for example a protein carrier, such as BSA. Such formulations are well-known to the person skilled in the art.

The peptides may be suppressor peptides normally lost or decreased in tumor tissue administered in order to stabilise tumors towards a less malignant stage. In another embodiment the peptides are onco-peptides capable of eliciting an immune response towards the tumor cells.

In another embodiment the pharmaceutical composition comprises genetic material, either genetic material for substitution therapy, or for suppressing therapy as discussed below.

In a third embodiment the pharmaceutical composition comprises at least one anti-body produced as described above.

In the present context the term pharmaceutical composition is used synonymously with the, term medicament. The medicament of the invention comprises an effective amount of one or more of the compounds as defined above, or a composition as defined above in combination with pharmaceutically acceptable additives. Such medicament may suitably be formulated for oral, percutaneous, intramuscular, intravenous, intracranial, intrathecal, intracerebroventricular, intranasal or pulmonal administration. For most indications a localised or substantially localised application is preferred.

Strategies in formulation development of medicaments and compositions based on the compounds of the present invention generally correspond to formulation strategies for any other protein-based drug product. Potential problems and the guidance required to overcome these problems are dealt with in several textbooks, e.g. “Therapeutic Peptides and Protein Formulation. Processing and Delivery Systems”, Ed. A. K. Banga, Technomic Publishing AG, Basel, 1995.

Injectables are usually prepared either: as liquid solutions or suspensions, solid forms suitable for solution in, or suspension in, liquid prior to injection. The preparation may also be emulsified. The active ingredient is often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol or the like, and combinations thereof. In addition, if desired, the preparation may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, or which enhance the effectiveness or transportation of the preparation.

Formulations of the compounds of the invention can be prepared by techniques known to the person skilled in the art. The formulations may contain pharmaceutically acceptable carriers and excipients including microspheres, liposomes, microcapsules and nanoparticles.

The preparation may suitably be administered by injection, optionally at the site, where the active ingredient is to exert its effect. Additional formulations which are suitable for other modes of administration include suppositories, and in some cases, oral formulations. For suppositories, traditional binders and carriers include polyalkylene glycols or triglycerides. Such suppositories may be formed from mixtures containing the active ingredient(s) in the range of from 0.5% to 10%, preferably 1-2%. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium, saccharine, cellulose, magnesium carbonate, and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formutations or powders and generally contain 10-95% of the active ingredient(s), preferably 25-70%.

The preparations are administered in a manner compatible with the dosage formulation, and in such amount as will be therapeutically effective. The quantity to be administered depends on the subject to be treated, including, e.g. the weight and age of the subject, the disease to be treated and the stage of disease. Suitable dosage ranges are of the order of several hundred μg active ingredient per administration with a preferred range of from about 0.1 μg to 1000 μg, such as in the range of from about 1 μg to 300 μg, and especially in the range of from about 10 μg to 50 μg. Administration may be performed once or may be followed by subsequent administrations. The dosage will also depend on the route of administration and will vary with the age and weight of the subject to be treated. A preferred dosis would be in the interval 30 mg to 70 mg per 70 kg body weight.

Some of the compounds of the present invention are sufficiently active, but for some of the others, the effect will be enhanced if the preparation further comprises pharmaceutically acceptable additives and/or carriers. Such additives and carriers will be known in the art. In some cases, it will be advantageous to include a compound, which promote delivery of the active substance to its target.

In many instances, it will be necessary to administrate the formulation multiple times. Administration may be a continuous infusion, such as intraventricular infusion or administration in more doses such as more times a day, daily, more times a week, weekly, etc.

Vaccines

In a further embodiment the present invention relates to a vaccine for the prophylaxis or treatment of a biological condition comprising at least one expression product from at least one gene said gene being expressed as defined above.

The term vaccines is used with its normal meaning, i.e preparations of immunogenic material for administration to induce in the recipient an immunity to infection or intoxication by a given infecting agent. Vaccines may be administered by intravenous injection or through oral, nasal and/or mucosal administration. Vaccines may be either simple vaccines prepared from one species of expression products, such as proteins or peptides, or a variety of expression products, or they may be mixed vaccines containing two or more simple vaccines. They are prepared in such a manner as not to destroy the immunogenic material, although the methods of preparation vary, depending on the vaccine.

The enhanced immune response achieved according to the invention can be attributable to e.g. an enhanced increase in the level of immunoglobulins or in the level of T-cells including cytotoxic T-cells will result in immunisation of at least 50% of individuals exposed to said immunogenic composition or vaccine, such as at least 55%, for example at least 60%, such as at least 65%, for example at least 70%, for example at least 75%, such as at least 80%, for example at least 85%, such as at least 90%, for example at least 92%, such as at least 94%, for example at least 96%, such as at least 97%, for example at least 98%, such as at least 98.5%, for example at least 99%, for example at least 99.5% of the individuals exposed to said immunogenic composition or vaccine are immunised.

Compositions according to the invention may also comprise any carrier and/or adjuvant known in the art including functional equivalents thereof. Functionally equivalent carriers are capable of presenting the same immunogenic determinant in essentially the same steric conformation when used under similar conditions. Functionally equivalent adjuvants are capable of providing similar increases in the efficacy of the composition when used under similar conditions.

Therapy

The invention further relates to a method of treating individuals suffering from the biological condition in question, in particular for treating a bladder tumor.

In one embodiment the invention relates to a method of substitution therapy, ie. administration of genetic material generally expressed in normal cells, but lost or decreased in biological condition cells (tumor suppressors). Thus, the invention relates to a method for reducing cell tumorigenicity or malignancy of a cell, said method comprising

-   obtaining at least one gene selected from genes being expressed in     an amount two-fold higher in normal cells than the amount expressed     in said tumor cell (tumor suppressors), -   introducing said at least one gene into the tumor cell in a manner     allowing expression of said gene(s).

The at least one gene is preferably selected individually from genes comprising a sequence as identified below

RC_AA158234_at zo76b01.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 592777 3′. RC_H42123_at yo61a11.s1 Homo sapiens cDNA clone 182396 3′. RC_Z39200_at H. sapiens partial cDNA sequence; clone c-13f02. RC_N21687_at yx63h03.s1 Soares melanocyte 2NbHM Homo sapiens cDNA clone 266453 3′. Y13645_at Homo sapiens mRNA for uroplakin II. RC_N98461_at zb86b03.s1 Soares senescent fibroblasts NbHSF Homo sapiens cDNA clone 310445 3′. RC_W92449_at zd99d10.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 357619 3′. RC_Z39191_at H. sapiens partial cDNA sequence; clone c-13c12. RC_AA125808_at zl29e12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 503374 3′. RC_T40767_at ya11a06.s1 Homo sapiens cDNA clone 61138 3′. RC_T51972_at yb29c05.s1 Homo sapiens cDNA clone 72584 3′. RC_AA286862_at zs58b06.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 701651 3′. RC_N29764_at yw91b09.s1 Homo sapiens cDNA clone 259577 3′. AA428172_f_at zw32b06.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 770963 5′. RC_H02265_at yj35d05.s1 Homo sapiens cDNA clone 150729 3′. RC_W44745_at zb98a11.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 320828 3′. RC_R91819_at yp99c05.s1 Homo sapiens cDNA clone 195560 3′ similar to contains MER1 repetitive element;. AA464468_at zx84d05.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810441 5′. RC_AA188647_at zp78e01.s1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 626328 3′ similar to TR: G998813 G998813 TIF1. [1];. RC_AA405832_at zu57g11.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 742148 3′ similar to TR: G780241 G780241 AU-BINDING PROTEIN/ENOYL-COA HYDRATASE.;. RC_W37778_f_at zc13b12.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322175 3′ similar to contains LTR2.t3 LTR2 repetitive element;. AF010126_at Homo sapiens breast cancer-specific protein 1 (BCSG1) mRNA, complete cds. N36432_at yx83a05.r1 Homo sapiens cDNA clone 268304 5′. RC_AA236533_s_(—) zr74c04.s1 Soares NhHMPu S1 Homo sapiens cDNA clone at 669126 3′ similar to gb: S69002 ECOTROPIC VIRUS INTEGRATION 1 SITE PROTEIN (HUMAN);. RC_AA293163_at zt55e05.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 726272 3′. RC_AA196790_at zq60b06.s1 Stratagene neuroepithelium (#937231) Homo sapiens cDNA clone 645971 3′. RC_AA253220_at zr53g12.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 667174 3′. RC_AA100437_at zn59e02.s1 Stratagene muscle 937209 Homo sapiens cDNA clone 562490 3′. RC_AA293300_s_(—) zt28d03.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 714437 3′. RC_Z39652_at H. sapiens partial cDNA sequence; clone c-1fg03. M63509_s_at Human glutathione transferase M2 (GSTM2) mRNA, complete cds RC_Z39842_at H. sapiens partial cDNA sequence; clone c-1ke11. RC_N23319_at yx78e10.s1 Homo sapiens cDNA clone 267882 3′. RC_AA278817_at zs78d11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 703605 3′. L20773_at Homo sapiens mRNA in the region near the btk gene involved in a-gamma-globulinemia RC_R69276_at yi44h05.s1 Soares placenta Nb2HP Homo sapiens cDNA clone 142137 3′. RC_F02641_at H. sapiens partial cDNA sequence; clone c-15d02. RC_AA424791_at zw03a04.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 768174 3′ similar to contains Alu repetitive element;. RC_R39869_at yf63b06.s1 Homo sapiens cDNA clone 26725 3′. RC_AA482224_f_(—) ab15c03.s1 Stratagene lung (#937210) Homo sapiens cDNA at clone 840868 3′. RC_AA025277_at ze76f02.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 364923 3′ similar to contains Alu repetitive element; contains element LTR4 repetitive element;. AA482319_f_at ab15c03.r1 Stratagene lung (#937210) Homo sapiens cDNA clone 840868 5′. RC_AA001045_at ze47b04.s1 Soares retina N2b4HR Homo sapiens cDNA clone 362095 3′. RC_AA130645_s_(—) zo10f03.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo at sapiens cDNA clone 567293 3′ similar to SW: NI2M_BOVIN Q02369 NADH-UBIQUINONE OXIDOREDUCTASE B22 SUBUNIT;. RC_AA291659_at zt37c02.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 724514 3′. AA046768_at zk72d02.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 488355 5′. H07011_at yl81e01.r1 Homo sapiens cDNA clone 44466 5′. RC_AA293533_i_(—) zt54g04.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 726198 3′ similar to gb: J05158 CARBOXYPEPTIDASE N 83 KD CHAIN (HUMAN);. RC_AA100649_at zn63g10.s1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 562914 3′ similar to SW: LCFA_ECOLI P29212 LONG-CHAIN-FATTY-ACID—COA LIGASE;. RC_AA017146_at ze41a07.s1 Soares retina N2b4HR Homo sapiens cDNA clone 361524 3′ similar to contains element PTR7 repetitive element;. RC_AA180054_at zp40g07.s1 Stratagene muscle 937209 Homo sapiens cDNA clone 611964 3′. AA263032_s_at PMY0335 KG1a Lambda Zap Express cDNA Library Homo sapiens cDNA 5′. W69310_at zd46f07.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 343717 5′. RC_AA219653_at zr05e02.s1 Stratagene NT2 neuronal precursor 937230 Homo sapiens cDNA clone 650618 3′. RC_AA457235_at aa91c07.s1 Stratagene fetal retina 937202 Homo sapiens cDNA clone 838668 3′. RC_AA455967_at aa16h10.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 813475 3′. N27670_at yx51a09.r1 Homo sapiens cDNA clone 265240 5′. RC_N80152_at za65e02.s1 Homo sapiens cDNA clone 297434 3′. RC_R64660_at yi22a10.s1 Homo sapiens cDNA clone 139962 3′. RC_AA147218_s_(—) zo64g03.s1 Stratagene pancreas (#937208) Homo sapiens at cDNA clone 591700 3′. C01139_at HUMGS0007818, Human Gene Signature, 3′-directed cDNA sequence. AA285284_at PMY0691 KG1a Lambda Zap Express cDNA Library Homo sapiens cDNA 5′. RC_AA451685_at zx44c03.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 789316 3′. AA203222_at zx56e01.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 446520 5′ similar to contains element MER17 repetitive element;. RC_AA394071_at zt52g01.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 726000 3′ similar to SW: ADG_MOUSE P22892 GAMMAADAPTIN;. RC_AA479096_at zv17e07.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 753924 3′. RC_AA156532_at zo34b05.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 588753 3′. RC_Z40233_at H. sapiens partial cDNA sequence; clone c-1wg05. RC_T03927_at seq2490 Homo sapiens cDNA clone 3HFLSK20-87 3′. AA314457_at EST186294 Colon carcinoma (HCC) cell line II Homo sapiens cDNA 5′ end. RC_N50550_at yy89f05.s1 Homo sapiens cDNA clone 280737 3′. RC_AA191524_at zp88f04.s1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 627295 3′. RC_N29740_at yw90b12.s1 Homo sapiens cDNA clone 259487 3′. RC_N48715_at yy75h02.s1 Homo sapiens cDNA clone 279411 3′. RC_AA463637_at zx98h04.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 811831 3′. RC_AA404487_at zw38a06.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 772306 3′. RC_H16666_at ym26a10.s1 Homo sapiens cDNA clone 49155 3′. RC_AA406197_at zv24d11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 754581 3′. RC_H09594_at yl97b11.s1 Homo sapiens cDNA clone 46276 3′. RC_AA161085_at zo62h09.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 591521 3′ similar to SW: PPAP_RAT P20646 PROSTATIC ACID PHOSPHATASE PRECURSOR;. RC_AA452131_at zx15d06.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 786539 3′. RC_AA293533_f_(—) zt54g04.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 726198 3′ similar to gb: J05158 CARBOXYPEPTIDASE N 83 KD CHAIN (HUMAN);. RC_AA398197_at zt59a08.s1 Soares testis NHT Homo sapiens cDNA clone 726614 3′. AA464051_s_at zx86d04.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810631 5′. RC_T51990_at yb29e01.s1 Homo sapiens cDNA clone 72600 3′. RC_AA236356_at zr54a11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 667196 3′. W92678_at zd92a04.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 356910 5′ similar to contains element LTR3 repetitive element;. RC_N63332_at yz33d11.s1 Homo sapiens cDNA clone 284853 3′ similar to contains Alu repetitive element;. C16281_s_at Human aorta cDNA 5′-end GEN-259H09. RC_AA477252_at zu29h10.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 739459 3′. H88035_s_at yw20e07.r1 Homo sapiens cDNA clone 252804 5′. AB002387_at Human mRNA for KIAA0389 gene, complete cds. RC_R45698_at yg45h12.s1 Homo sapiens cDNA clone 35838 3′. RC_AA236542_at zr75g11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 669284 3′. AA376875_at EST89388 Small intestine I Homo sapiens cDNA 5′ end similar to monoamine oxidase A. RC_R43365_at yg15g06.s1 Homo sapiens cDNA clone 32365 3′. RC_H06746_at yl83h08.s1 Homo sapiens cDNA clone 44847 3′. RC_AA233837_at zr47f06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 666563 3′. RC_AA057620_at zf15h06.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 377051 3′. RC_AA450118_at zx42e09.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 789160 3′. RC_AA598872_at ae37b10.s1 Gessler Wilms tumor Homo sapiens cDNA clone 897979 3′. RC_AA147646_s_(—) zl52g06.s1 Soares pregnant uterus NbHPU Homo sapiens at cDNA clone 505594 3′. RC_W04698_at zb94b05.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 320433 3′. RC_N54365_at yv39c06.s1 Homo sapiens cDNA clone 245098 3′. RC_AA256208_at zr80a08.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 681974 3′. AA046593_at zk62g01.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 487440 5′. RC_AA002088_at zh85g03.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 428116 3′. RC_AA256273_at zr81c12.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 682102 3′. AA491114_at aa46e04.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 823998 5′. RC_AA293719_at zt55h03.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 726293 3′. RC_AA086005_at zl84c04.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 511302 3′. RC_AA479885_at zw44a07.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 772884 3′. AA442428_at zv70f08.r1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 759015 5′ similar to SW: YB72_YEAST P38137 HYPOTHETICAL 60.5 KD PROTEIN IN PDB1-ABD1 INTERGENIC REGION. ;. RC_AA486410_at ab36b12.s1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842879 3′. R15268_at yf89f02.r1 Homo sapiens cDNA clone 29665 5′. RC_AA443658_at zw86a10.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 783834 3′ similar to TR: G438639 G438639 LAMIN B RECEPTOR. [1];. RC_H16790_at ym39b01.s1 Homo sapiens cDNA clone 50559 3′. AA465000_s_at zx80b07.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810037 5′. RC_N38930_at yy43e04.s1 Homo sapiens cDNA clone 274014 3′. AB002321_at Human mRNA for KIAA0323 gene, partial cds. RC_Z38810_at H. sapiens partial cDNA sequence; clone c-0qb09. AC000115_cds1_(—) WUGSC: H_GS188P18.1a gene extracted from Human BAC at clone GS188P18 RC_AA255464_at zr83b02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 682251 3′. RC_AA255628_at zs31g06.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 686842 3′. RC_H70554_at yr91a03.s1 Homo sapiens cDNA clone 212620 3′. AA309880_at EST180743 Jurkat T-cells V Homo sapiens cDNA 5′ end. RC_R43812_at yg21a08.s1 Homo sapiens cDNA clone 32940 3′. RC_AA425636_at zv47a04.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 756750 3′. RC_N66388_at yz39f01.s1 Homo sapiens cDNA clone 285433 3′. RC_AA279420_at zs85d09.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 704273 3′ similar to TR: G974805 G974805 T08A11.2;. RC_AA033974_at zi05c10.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 429906 3′. AF007216_at Homo sapiens sodium bicarbonate cotransporter (HNBC1) mRNA, complete cds. RC_AA489101_at aa56h11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 824997 3′. D79601_f_at Human aorta cDNA 5′-end GEN-286G10. RC_N30856_at yw70f05.s1 Homo sapiens cDNA clone 257601 3′. L29218_s_at Homo sapiens clk2 mRNA, complete cds RC_AA143726_at zo67g06.s1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 591994 3′ similar to TR: G530823 G530823 EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE. ;. AA126592_at zl17g05.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 502232 5′. RC_F02397_s_at H. sapiens partial cDNA sequence; clone c-0xh11. RC_AA252765_at zs27d03.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 686405 3′. RC_W46846_at zc36a04.s1 Soares senescent fibroblasts NbHSF Homo sapiens cDNA clone 324366 3′. RC_AA135185_at zo27a05.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 588080 3′. RC_R40702_at yf73f10.s1 Homo sapiens cDNA clone 27969 3′. RC_N52565_at yv36d12.s1 Homo sapiens cDNA clone 244823 3′. RC_W32506_s_at zc06a02.s1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 321482 3′. RC_AA255539_at zr85c04.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 682470 3′. RC_AA449951_at zx38a10.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 788730 3′. AA091278_at cchn2404.seq.F Fetal heart, Lambda ZAP Express Homo sapiens cDNA 5′. RC_AA236037_at zs05g08.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 684350 3′. AA091412_s_at II2053.seq.F Fetal heart, Lambda ZAP Express Homo sapiens cDNA 5′. AA046865_at zf12b09.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 376697 5′. AA324825_at EST27743 Cerebellum II Homo sapiens cDNA 5′ end. RC_AA454840_s_(—) zx79d09.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 809969 3′. RC_W80354_at zh49a02.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 415370 3′. RC_AA402484_at zt65c03.s1 Soares testis NHT Homo sapiens cDNA clone 727204 3′. W26883_at 15h10 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA. RC_AA262485_at zs17h07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 685501 3′. RC_AA405543_at zw39c01.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 772416 3′. RC_N21380_at yx54c04.s1 Homo sapiens cDNA clone 265542 3′. RC_AA121360_s_(—) zn77a05.s1 Stratagene NT2 neuronal precursor 937230 Homo at sapiens cDNA clone 564176 3′. L32832_s_at Homo sapiens zinc finger homeodomain protein (ATBF1-A) mRNA, complete cds. D31313_s_at Human fetal-lung cDNA 5′-end sequence. H18718_at ym45b05.r1 Homo sapiens cDNA clone 51043 5′ similar to contains Alu repetitive element;. RC_AA037828_at zf03g09.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 375904 3′. RC_R67996_at yi04c10.s1 Homo sapiens cDNA clone 138258 3′. RC_AA026417_at ze92g08.s1 Soares fetal heart NbHHI9W Homo sapiens cDNA clone 366494 3′. RC_F11115_at H. sapiens partial cDNA sequence; clone c-33a10. RC_R08871_at yf21e07.s1 Homo sapiens cDNA clone 127524 3′. RC_AA224324_at zr12e05.s1 Stratagene hNT neuron (#937233) Homo sapiens cDNA clone 648608 3′. RC_AA399226_at zt50c01.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 725760 3′. R66920_at yi25f09.r1 Homo sapiens cDNA clone 140297 5′ similar to contains Alu repetitive element;. RC_AA464240_s_(—) zx81a05.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 810128 3′. AA436536_at zv08g07.r1 Soares NhHMPu S1 Homo sapiens cDNA clone 753084 5′. RC_N71875_at yz34f07.s1 Homo sapiens cDNA clone 284965 3′. RC_AA029288_at zk10b03.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 470093 3′ similar to PIR: H45193 H45193 zinc finger protein ZNF65;. H27242_at yl63h11.r1 Homo sapiens cDNA clone 162981 5′ similar to SP: GCN5_YEAST Q03330 TRANSCRIPTIONAL ACTIVATOR;. J04813_s_at Human cytochrome P450 PCN3 gene, complete cds RC_AA465093_at aa32h08.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 815007 3′. RC_AA282791_at zs91c05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 704840 3′. RC_AA464180_at zx83f04.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810367 3′ similar to gb: M38188 OVARIAN GRANULOSA CELL 13.0 KD PROTEIN HGR74 (HUMAN);. RC_AA149987_at zo03d03.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 566597 3′. RC_AA256680_at zr82h09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 682241 3′. AA147510_s_at zl50c12.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 505366 5′. R78119_at yi80c10.r1 Homo sapiens cDNA clone 145554 5′. RC_Z38407_s_at H. sapiens partial cDNA sequence; clone c-0ac03. RC_AA287107_s_(—) zs58f12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone at IMAGE: 701711 3′. RC_AA287042_at zs57e07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 701604 3′. AA489299_at ab35g04.r1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842838 5′. AA504744_at aa63f03.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 825629 5′. RC_AA402622_at zu47g07.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 741180 3′. RC_AA436628_at zw55e10.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 773994 3′. RC_AA282138_at zt02a10.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 711930 3′. AA045870_at zk75a04.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 488622 5′. AA418098_at zv94b04.r1 Soares NhHMPu S1 Homo sapiens cDNA clone 767407 5′. RC_AA242799_at zr65f06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 668291 3′ similar to SW: SPO8_YEAST P41833 TRANSCRIPTIONAL REGULATOR SPO8. [1];. RC_AA609210_at af12f04.s1 Soares testis NHT Homo sapiens cDNA clone 1031455 3′. RC_AA133469_at zo13e11.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 586796 3′. R22139_at yh25b11.r1 Homo sapiens cDNA clone 130749 5′. AA305116_at EST176117 Colon carcinoma (Caco-2) cell line II Homo sapiens cDNA 5′ end. RC_AA027954_at zk05c12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 469654 3′. AA036900_at zk29e11.r1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 471980 5′. RC_AA026397_at ze92d07.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 366445 3′. RC_D59981_s_at Human fetal brain cDNA 3′-end GEN-079C04. RC_AA284143_at zs47c07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 700620 3′. W16686_at zb08f12.r1 Soares fetal lung NbHL19W Homo sapiens cDNA clone 301487 5′. H89575_s_at yw28c11.r1 Homo sapiens cDNA clone 253556 5′. RC_AA251003_at zs07g11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 684548 3′. RC_AA279408_at zs84h09.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 704225 3′. RC_AA281760_at zt07g10.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 712482 3′ similar to TR: G808826 G808826 HYPOTHETICAL 25.7 KD PROTEIN.;. AB002381_at Human mRNA for KIAA0383 gene, partial cds. AA459542_s_at zx89d08.r1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 810927 5′ similar to TR: G608025 G608025 ANKYRING.;. RC_AA115559_at zl07b12.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA clone 491615 3′. T94506_at ye36a05.r1 Homo sapiens cDNA clone 119792 5′. D55869_s_at Human fetal brain cDNA 5′-end GEN-404F02. L02547_at Homo sapiens (clone pZ50-19) cleavage stimulation factor 50 kDa subunit, complete cds U77942_at Human syntaxin 7 mRNA, complete cds. AA431505_at zw76e03.r1 Soares testis NHT Homo sapiens cDNA clone 782140 5′. RC_AA194045_at zr38c08.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 665678 3′. RC_AA025104_at ze78f05.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 365121 3′. RC_AA242822_at zr65e09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 668296 3′. RC_AA287388_at zs50f04.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 700927 3′. AA247679_at hfe0045.seq.F Human fetal heart, Lambda ZAP Express Homo sapiens cDNA 5′. RC_AA489383_at ab41e08.s1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 843398 3′. RC_AA621188_at zu81a08.s1 Soares testis NHT Homo sapiens cDNA clone 744374 3′. RC_AA486182_at ab35a01.s1 Stratagene HeLa cell s3 937216 Homo sapiens cDNA clone 842760 3′. RC_AA393876_s_(—) zv64h10.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA at clone 758467 3′. RC_AA034189_at zi06h12.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 430055 3′. RC_AA024866_at ze79b09.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 365177 3′. RC_AA450373_at zx05h06.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 785627 3′. N78483_at yz78d07.r1 Homo sapiens cDNA clone 289165 5′. RC_AA281245_at zs94d07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone IMAGE: 705133 3′. W52431_at zc45b12.r1 Soares senescent fibroblasts NbHSF Homo sapiens cDNA clone 325247 5′ similar to SW: WDNM_RAT P14730 WDNM1 PROTEIN. [2] PIR: S07807;. RC_AA446597_at zw84f01.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA clone 783673 3′. RC_AA256996_at zr81h11.s1 Soares NhHMPu S1 Homo sapiens cDNA clone 682149 3′. X73501_at H. sapiens gene for cytokeratin 20 RC_AA287131_at zt20g02.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone 713714 3′ similar to TR: E124071 E124071 NAD +− ISOCITRATE DEHYDROGENASE;. or from a sequence as identified below

AB002370_at Human mRNA for KIAA0372 gene, complete cds. AF000546_at Homo sapiens purinergic receptor P2Y5 mRNA, complete cds. H43922_at yo70c03.r1 Homo sapiens cDNA clone 183268 5′. H44269_at yp17b05.r1 Homo sapiens cDNA clone 187665 5′ similar to contains Alu repetitive element;. H88706_s_at yw23e08.r1 Homo sapiens cDNA clone 253094 5′. L25880_s_at Homo sapiens epoxide hydrolase (EPHX) gene, complete cds N81162_at yw36d01.r1 Homo sapiens cDNA clone 254305 5′. RC_F10381_s_at H. sapiens partial cDNA sequence; clone c-3ec07. RC_H54558_at EST00018 HE6W Homo sapiens cDNA clone HE6WCR108 3′. RC_H58692_s_(—) yr20g08.s1 Homo sapiens cDNA clone 205886 3′ similar to at SP: FTDH_RAT P28037 FORMYLTETRAHYDROFOLATE DEHYDROGENASE;. RC_N20047_at yx28d06.s1 Homo sapiens cDNA clone 263051 3′. RC_N38810_at yv28e04.s1 Homo sapiens cDNA clone 244062 3′. RC_R46497_at yg51h01.s1 Homo sapiens cDNA clone 36305 3′. RC_R55001_at yj76a08.s1 Homo sapiens cDNA clone 154646 3′. RC_T29986_s_at EST10130 Homo sapiens cDNA 3′ end similar to None. RC_T30214_at EST12901 Homo sapiens cDNA 3′ end similar to None. RC_T40438_at ya01c07.s2 Homo sapiens cDNA clone 60204 3′. RC_W51910_at zc37f06.s1 Soares senescent fibroblasts NbHSF Homo sapiens cDNA clone 324515 3′. RC_W73949_at zd71f09.s1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 346121 3′. RC_W86375_s_(—) zh55a02.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens at cDNA clone 415946 3′. RC_Z38289_at H. sapiens partial cDNA sequence; clone c-05e04. RC_Z38807_s_at H. sapiens partial cDNA sequence; clone c-0qb04. RC_Z39599_at H. sapiens partial cDNA sequence; clone c-1ed10. RC_AA025351_(—) ze74h03.s1 Soares fetal heart NbHH19W Homo sapiens cDNA at clone 364757 3′ similar to contains OFR.t1 OFR repetitive element;. RC_AA136474_(—) zl01f04.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA at clone 491071 3′. RC_AA136611_(—) zk99b02.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA at clone 490923 3′. RC_AA233375_(—) zr48f07.s1 Soares NhHMPu S1 Homo sapiens cDNA clone at 666661 3′. RC_AA235621_(—) zt36c05.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone s_at 724424 3′. RC_AA253331_(—) zr72g02.s1 Soares NhHMPu S1 Homo sapiens cDNA clone at 668978 3′. RC_AA393793_(—) zv64a10.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA at clone 758394 3′. RC_AA419547_(—) zv04a05.s1 Soares NhHMPu S1 Homo sapiens cDNA clone at 752624 3′. RC_AA421100_(—) zu27d11.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 739221 3′. RC_AA443277_(—) zw87f06.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA at clone 783971 3′. RC_AA446570_(—) zw84c05.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA at clone 783656 3′. RC_AA447123_(—) zw93c01.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA at clone 784512 3′. RC_AA449343_(—) zx06g09.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA at clone 785728 3′. RC_AA456016_(—) aa03a08.s1 Soares NhHMPu S1 Homo sapiens cDNA clone at 812150 3′. RC_AA479299_(—) zv21f04.s1 Soares NhHMPu S1 Homo sapiens cDNA clone at 754303 3′. RC_AA479350_(—) zv17d09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone at 753905 3′ similar to contains element TAR1 TAR1 repetitive element;. U85707_at Human leukemogenic homolog protein (MEIS1) mRNA, complete cds U94831_at Human multispanning membrane protein mRNA, complete cds./ gb = U94831/ntype = RNA W27827_at 38c8 Human retina cDNA randomly primed sublibrary Homo sapiens cDNA. W81301_at zd85a12.r1 Soares fetal heart NbHH19W Homo sapiens cDNA clone 347422 5′. Y12711_at H. sapiens mRNA for putative progesterone binding protein AA074407_at zm15c08.r1 Stratagene pancreas (#937208) Homo sapiens cDNA clone 525710 5′. AA091017_at yy1646.seq.F Fetal heart, Lambda ZAP Express Homo sapiens cDNA 5′. AA104023_at l7134.seq.F Fetal heart, Lambda ZAP Express Homo sapiens cDNA 5′. AA171913_at zo95d05.r1 Stratagene ovarian cancer (#937219) Homo sapiens cDNA clone 594633 5′. AA195678_at zr32h05.r1 Soares NhHMPu S1 Homo sapiens cDNA clone 665145 5′. AA227678_at zr55e05.r1 Soares NhHMPu S1 Homo sapiens cDNA clone 667328 5′. AA247204_at csg0306.seq.F Human fetal heart, Lambda ZAP Express Homo sapiens cDNA 5′. AA479995_at zv18b05.r1 Soares NhHMPu S1 Homo sapiens cDNA clone 753969 5′. or from a sequence as identified below

RC_H14633_at yl26e06.s1 Homo sapiens cDNA clone 159394 3′. RC_N62506_at yz74d02.s1 Homo sapiens cDNA clone 288771 3′. RC_N70481_at za74g10.s1 Homo sapiens cDNA clone 298338 3′. RC_N73988_at za57b06.s1 Homo sapiens cDNA clone 296627 3′. RC_T53404_at ya88g06.s1 Homo sapiens cDNA clone 68794 3′. RC_Z38149_at H. sapiens partial cDNA sequence; clone c-01a09. RC_Z38849_at H. sapiens partial cDNA sequence; clone c-0rb11. RC_AA037409_(—) zc03h03.s1 Soares parathyroid tumor NbHPA Homo sapiens at cDNA clone 321269 3′. RC_AA084318_(—) zn18b04.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo at sapiens cDNA clone 547759 3′. RC_AA126419_(—) zk94d04.s1 Soares pregnant uterus NbHPU Homo sapiens cDNA at clone 490471 3′. RC_AA128407_(—) zm24d04.s1 Stratagene pancreas (#937208) Homo sapiens at cDNA clone 526567 3′. RC_AA173430_(—) zp02e08.s1 Stratagene ovarian cancer (#937219) Homo sapiens at cDNA clone 595238 3′. RC_AA398104_(—) zt58d03.s1 Soares testis NHT Homo sapiens cDNA clone 726533 at 3′. RC_AA399414_(—) zt50e07.s1 Soares ovary tumor NbHOT Homo sapiens cDNA clone at 725796 3′. RC_AA431479_(—) zw72f05.s1 Soares testis NHT Homo sapiens cDNA clone 781761 at 3′. RC_AA436471_(—) zv08e05.s1 Soares NhHMPu S1 Homo sapiens cDNA clone at 753056 3′. RC_AA449455_(—) zx05e10.s1 Soares total fetus Nb2HF8 9w Homo sapiens cDNA at clone 785610 3′ similar to contains Alu repetitive element;. RC_AA458899_(—) zx88d07.s1 Soares ovary tumor NbHOT Homo sapiens cDNA at clone 810829 3′. RC_AA463630_(—) zx98g09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone s_at 811840 3′. RC_AA489009_(—) aa54d11.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone at IMAGE: 824757 3′. W37319_at zc11f08.r1 Soares parathyroid tumor NbHPA Homo sapiens cDNA clone 322023 5′. or from a sequence as identified below

yx16e10.r1 Homo sapiens cDNA clone 261930 5′. N24990_s_at yf41e08.r1 Homo sapiens cDNA clone 129446 5′ similar to R11267_at SP: A46661 A46661 LEUKOTRIENE B4 OMEGA- HYDROXYLASE, P-450LTB OMEGA = CYTOCHROME P-450 SUPERFAMILY MEMBER-;. yq76e12.s1 Homo sapiens cDNA clone 201742 3′ similar to RC_H52937_at gb: J02982 GLYCOPHORIN B PRECURSOR (HUMAN);. yr89e02.s1 Homo sapiens cDNA clone 212474 3′. RC_H69547_at yu73c12.s1 Homo sapiens cDNA clone 239446 3′. RC_H70047_at yx99c11.s1 Homo sapiens cDNA clone 269876 3′. RC_N24879_at yz38a06.s1 Homo sapiens cDNA clone 285298 3′. RC_N66312_at yh26a02.s1 Homo sapiens cDNA clone 130826 3′. RC_R22189_at yg44f05.s1 Homo sapiens cDNA clone 35270 3′. RC_R45582_at yg83e10.s1 Homo sapiens cDNA clone 39835 3′. RC_R53457_at yi49g10.s1 Homo sapiens cDNA clone 142626 3′. RC_R70903_at zl68c01.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA054321_s_at clone 509760 3′. zk87c05.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA099820_at cDNA clone 489800 3′. zl17g05.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA127238_at cDNA clone 502232 3′. zo64h02.s1 Stratagene pancreas (#937208) Homo sapiens RC_AA147224_at cDNA clone 591699 3′. zq12e02.s1 Stratagene muscle 937209 Homo sapiens cDNA RC_AA192765_at clone 629498 3′. zr33d07.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA195718_at 665197 3′. zr28b08.s1 Stratagene NT2 neuronal precursor 937230 Homo RC_AA232114_s_at sapiens cDNA clone 664695 3′ similar to gb: L05779 SOLUBLE EPOXIDE HYDROLASE (HUMAN);. zt07h12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA281770_at IMAGE: 712487 3′. zw59e03.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA430209_at cDNA clone 774364 3′ similar to TR: G1199667 G1199667 PROTEIN KINASE C-BINDING PROTEIN ENIGMA;. zx31f03.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA452410_at cDNA clone 788093 3′. aa39g12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA485115_at IMAGE: 815686 3′. zk85e12.r1 Soares pregnant uterus NbHPU Homo sapiens AA099391_s_at cDNA clone 489646 5′. zo16a05.r1 Stratagene colon (#937204) Homo sapiens cDNA AA131127_at clone 587024 5′ similar to SW: CATX_BOVIN P05689 CATHEPSIN;. zp02c06.r1 Stratagene ovarian cancer (#937219) Homo sapiens AA173505_at cDNA clone 595210 5′ similar to SW: QRI2_YEAST P43124 HYPOTHETICAL 46.1 KD PROTEIN IN PHO2-POL3 INTERGENIC REGION. [1];. zt39b07.r1 Soares ovary tumor NbHOT Homo sapiens cDNA AA291786_s_at clone 724693 5′. zu53f10.r1 Soares ovary tumor NbHOT Homo sapiens cDNA AA402971_s_at clone 741739 5′. or from a sequence as identified below

Human mRNA for IgG Fc binding protein, complete cds D84239_at yv73b09.s1 Soares fetal liver spleen 1NFLS Homo sapiens RC_N54841_at cDNA clone 248345 3′. ya88f04.s1 Home sapiens cDNA clone 68767 3′. RC_T53389_s_at ye30d12.s1 Homo sapiens cDNA clone 119255 3′. RC_T98227_at zr97c07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA215379_at IMAGE: 683628 3′. zr81e12.s1 Soares NhHMPu S1 Home sapiens cDNA clone RC_AA256485_at 682126 3′. zt19f03.s1 Soares ovary tumor NbHOT Home sapiens cDNA RC_AA290679_at clone 713597 3′ similar to TR: E92665 E92665 AP56;. zw46c01.s1 Soares total fetus Nb2HF8 9w Home sapiens RC_AA425309_at cDNA clone 773088 3′. zw71d04.s1 Soares testis NHT Homo sapiens cDNA clone RC_AA429655_at 781639 3′. aa90h11.s1 Stratagene fetal retina 937202 Homo sapiens RC_AA456981_at cDNA clone 838629 3′ similar to contains Alu repetitive element;. zx70c04.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA461174_at cDNA clone 796806 3′. zd27g09.r1 Soares fetal heart NbHH19W Homo sapiens W61377_at cDNA clone 341920 5′.

In one embodiment at least one gene is introduced into the tumor cell. In another embodiment at least two genes are introduced into the tumor cell.

In one aspect of the invention small molecules that either inhibit increased gene expression or their effects or substitute decreased gene expression or their effects, are introduced to the cellular environment or the cells. Application of small molecules to tumor cells may be performed by e.g. local application or intravenous injection or by oral ingestion. Small molecules have the ability to restore function of reduced gene expression in tumor or cancer tissue.

In another aspect the invention relates to a therapy whereby genes (increase and/or decrease) generally are correlated to disease are inhibited by one or more of the following methods:

A method for reducing cell tumorigenicity or malignancy of a cell, said method comprising

-   obtaining at least one nucleotide probe capable of hybridising with     at least one gene of a tumor cell, said at least one gene being     selected from genes being expressed in an amount at least one-fold     lower in normal cells than the amount expressed in said tumor cell,     and -   introducing said at least one nucleotide probe into the tumor cell     in a manner allowing the probe to hybridise to the at least one     gene, thereby inhibiting expression of said at least one gene. This     method is preferably based on anti-sense technology, whereby the     hybridisation of said probe to the gene leads to a downregulation of     said gene.

The down-regulation may of course also be based on a probe capable of hybridising to regulatory components of the genes in question, such as promoters.

The probes are preferably selected from probes capable of hybridising to a nucleotide sequence comprising a sequence as identified below

Homo sapiens mRNA for CC chemokine, complete cds. AB000221_at Human fetal brain cDNA 3′-end GEN-097D06. RC_D60296_at Human fetal brain cDNA 3′-end GEN-132E11. RC_D60813_at yg71a11.s1 Homo sapiens cDNA clone 38542 3′. RC_R49708_s_at H. sapiens partial cDNA sequence; clone c-02a08. RC_Z38182_at aa38e07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA456821_at IMAGE: 815556 3′; ae53d05.s1 Stratagene lung carcinoma 937218 Homo sapiens RC_AA608545_at cDNA clone 950601 3′. ae58g12.s1 Stratagene lung carcinoma 937218 Homo sapiens RC_AA620553_s_at cDNA clone 951142 3′. cp3087.seq.F Fetal heart, Lambda ZAP Express Homo sapiens AA095119_at cDNA 5′. or from

yn53b04.s1 Homo sapiens cDNA clone 172111 3′. RC_H20269_at H. sapiens partial cDNA sequence; clone c-2ea12. RC_Z40715_at zm79a11.s1 Stratagene neuroepithelium (#937231) Homo sapiens RC_AA116036_at cDNA clone 531836 3′. zn92a08.s1 Stratagene lung carcinoma 937218 Homo sapiens RC_AA133250_at cDNA clone 565622 3′. or from a sequence as identified below

Human threonyl-tRNA synthetase mRNA, complete cds M63180_at HFBEST-40 Human fetal brain QBoqin2 Homo sapiens cDNA. N89563_s_at Human fetal brain cDNA 3′-end GEN-045C11. RC_D80198_at H. sapiens partial cDNA sequence; clone c-0kf11. RC_F01986_f_at yn51g07.s1 Homo sapiens cDNA clone 171996 3′. RC_H18997_at zn76c11.s1 Stratagene NT2 neuronal precursor 937230 Homo RC_AA101562_at sapiens cDNA clone 564116 3′ similar to contains Alu repetitive. element;. or from a sequence as identified below

Ye73c08.s1 Homo sapiens cDNA clone 123374 3′. RC_R00083_at yj80e01.s1 Homo sapiens cDNA clone 155064 3′. RC_R71391_at Seq2147 Homo sapiens cDNA clone NHB3MK-9 3′. RC_T23991_at Yd70f06.s1 Homo sapiens cDNA clone 113603 3′ similar to RC_T79196_at contains Alu repetitive element;. Zo26a09.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA130596_at clone 587992 3′. Zx89d06.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA459310_r_at clone 810923 3′. aa48f12.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA490965_at IMAGE: 824207 3′. Human DNA binding protein homolog (DRX) mRNA, partial U88047_at cds Human DSC2 mRNA for desmocollins type 2a and 2b X56807_at zi01b10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens AA011479_at cDNA clone 429499 5′. EST112387 Aorta endothelial cells Homo sapiens cDNA 5′ AA296821_at end. or from a sequence as identified below

zx58c10.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens AA203639_at cDNA clone 446706 5′ similar to contains Alu repetitive element;. Human prealbumin gene, complete cds. M11844_at zq77f02.s1 Stratagene hNT neuron (#937233) Homo sapiens RC_AA206042_at cDNA clone 647643 3′ similar to contains element MSR1 repetitive element;. yz03e04.s1 Homo sapiens cDNA clone 281982 3′. RC_N51097_at yl70f08.s1 Soares infant brain 1NIB Homo sapiens cDNA clone RC_H05527_at 43327 3′. zl05d11.r1 Soares pregnant uterus NbHPU Homo sapiens AA115572_s_at cDNA clone 491445 5′ similar to TR: G895845 G895845 PUTATIVE P64 CLCP PROTEIN.;. yj14b12.s1 Homo sapiens cDNA clone 148703 3′. RC_H12863_at ab36e04.r1 Stratagene HeLa cell s3 937216 Homo sapiens AA489287_at cDNA clone 842910 5′. ye49h07.s1 Homo sapiens cDNA clone 121117 3′. RC_T96383_at yq98g12.s1 Homo sapiens cDNA clone 203878 3′. RC_H56453_at zl03h01.s1 Soares pregnant uterus-NbHPU Homo sapiens RC_AA152194_at cDNA clone 491281 3′. H. sapiens partial cDNA sequence; clone c-0ed05. RC_Z38520_at yd06g09.s1 Homo sapiens cDNA clone 25061 3′ similar to RC_R38944_at contains Alu repetitive element;. zo16e11.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA133926_at clone 587084 3′. za68f06.s1 Homo sapiens cDNA clone 297731 3′ similar to RC_N69908_f_at gb: X59244 ZINC FINGER PROTEIN 43 (HUMAN);. zo02c02.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA151945_at clone 566498 3′ similar to contains Alu repetitive element;. SOX5 = Sry-related HMG box gene {alternatively spliced} [human, S83308_at testis, mRNA, 1473 nt] zv11b06.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA406570_at 753299 3′. zl67g04.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA058314_at clone 509718 3′ similar to contains Alu repetitive element; contains element PTR5 repetitive element;. yr31g12.s1 Homo sapiens cDNA clone 206950 3′. RC_R98735_at or from a sequence as identified below

Human mRNA for KIAA0180 gene, partial cds D80002_at Similar to none. D82418_at Yx59d10.r1 Homo sapiens cDNA clone 266035 5′. N28843_at H. sapiens partial cDNA sequence; clone c-12c11. RC_F02541_at Yw65f02.s1 Homo sapiens cDNA clone 257115 3′. RC_N30806_at Yh81f02.s1 Homo sapiens cDNA clone 136155 3′ RC_R33146_at similar to contains Alu repetitive element;. Yf70a09.s1 Homo sapiens cDNA clone 27448 3′. RC_R40166_at Yi23g09.s1 Homo sapiens cDNA clone 140128 3′. RC_R65998_at Zk05c04.s1 Soares pregnant uterus NbHP RC_AA027823_at Homo sapiens cDNA clone 469638 3′. Zn17a03.s1 Stratagene neuroepithelium NT2RAMI RC_AA084138_at 937234 Homo sapiens cDNA clone 547660 3′. Zr13a10.s1 Stratagene hNT neuron (#937233) Homo RC_AA223902_at sapiens cDNA clone 648666 3′. Zv90g02.s1 Soares NhHMPu S1 Homo sapiens RC_AA424524_at cDNA clone 767090 3′. Aa65d11.s1 NCI_CGAP_GCB1 RC_AA505136_at Homo sapiens cDNA clone IMAGE: 825813 3′. Zk55g12.r1 Soares pregnant uterus NbHPU AA043223_at Homo sapiens cDNA clone 486790 5′. or from a sequence as identified below

H. sapiens partial cDNA sequence; clone c-1pb12. RC_F03192_at Zd87g10.s1 Soares fetal heart NbHH19W Homo sapiens RC_W81552_at cDNA clone 347682 3′. H. sapiens partial cDNA sequence; clone c-10c01. RC_F02470_at zc20b06.s1 Soares senescent fibroblasts NbHSF Homo sapiens RC_W44927_at cDNA clone 322835 3′ similar to PIR: S44218 S44218 testin - mouse [1];. yg46b01.s1 Homo sapiens cDNA clone 35626 3′. RC_R45292_at yr47b09.s1 Homo sapiens cDNA clone 208409 3′ similar to RC_H62159_at contains Alu repetitive element; contains MER15 repetitive element;. yf45a10.s2 Homo sapiens cDNA clone 129786 3′. RC_R17059_at ym30c10.s1 Homo sapiens cDNA clone 49795 3′. RC_H15259_at 29a6 Human retina cDNA randomly primed sublibrary Homo W26376_at sapiens cDNA. H. sapiens mRNA for putative carboxylesterase Y09616_at zw48f02.r1 Soares total fetus Nb2HF8 9w Homo sapiens AA425593_at cDNA clone 773307 5′. zt08e05.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA279980_at IMAGE: 712544 3′. ym62c07.s1 Homo sapiens cDNA clone 163500 3′. RC_H14089_at yg49c02.s1 Homo sapiens cDNA clone 36133 3′. RC_R46079_f_at zc17d10.s1 Soares parathyroid tumor NbHPA Homo sapiens RC_W15360_at cDNA clone 322579 3′ similar to PIR: S39983 S39983 eps8 protein - mouse;. Human mRNA for retinoic acid receptor-like protein X52773_at ze75b05.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA053886_s_at cDNA clone 364785 3′ similar to TR: G451330 G451330 STEROL REGULATORY ELEMENT BINDING PROTEIN-2.;. zo31a10.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA143493_at clone 588474 3′. Homo sapiens mRNA; expressed sequence tag; clone RC_Z98492_at DKFZphsnu1_1b13, 3′ read. H. sapiens partial cDNA sequence. F15201_at yh10f08.s1 Homo sapiens cDNA clone 42872 3′. RC_R61883_at 30e12 Human retina cDNA randomly primed sublibrary Homo W26505_at sapiens cDNA. zn53e03.s1 Stratagene muscle 937209 Homo sapiens cDNA RC_AA085676_at clone 561916 3′. ze55c07.r1 Soares retina N2b4HR Homo sapiens cDNA clone AA018804_at 362892 5′ similar to SW: RB14_RAT P35287 RAS- RELATED PROTEIN RAB-14. [1];. Human class I histocompatibility antigen-like protein mRNA, U22963_at complete cds. yf26d08.s1 Homo sapiens cDNA clone 127983 3′. RC_R09230_at yi25g01.s1 Homo sapiens cDNA clone 140304 3′. RC_R67918_at zu55d04.r1 Soares ovary tumor NbHOT Homo sapiens cDNA AA402119_at clone 741895 5′ similar to TR: G397579 G397579 LL5 MRNA. zn42g07.r1 Stratagene endothelial cell 937223 Homo sapiens AA082171_at cDNA clone 550140 5′. yi89d09.r1 Homo sapiens cDNA clone 146417 5′. R79750_at zw80d04.s1 Soares testis NHT Homo sapiens cDNA clone RC_AA431773_at 782503 3′. zs97a07.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone RC_AA280670_at IMAGE: 711540 3′. EST16378 Aorta endothelial cells, TNF alpha-treated Homo AA303711_at sapiens cDNA 5′ end. zu64g03.r1 Soares testis NHT Homo sapiens cDNA clone AA400361_at 742804 5′. Homo sapiens MDM2-like p53-binding protein (MDMX) AF007111_at mRNA, complete cds. aa59c02.r1 NCI_CGAP_GCB1 Homo sapiens cDNA clone AA504384_at IMAGE: 825218 5′ similar to contains element MIR repetitive element K1565F Fetal heart, Lambda ZAP Express Homo sapiens N88108_at cDNA clone K1565 5′ similar to EST(YD54C09.R1). aa20e01.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA447769_at 813816 3′. or from a sequence as identified below

Ze92h01.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA026418_at cDNA clone 366481 3′. Human fetal brain cDNA 3′-end GEN-070G07. RC_D59847_at Seq2287 Homo sapiens cDNA clone Cot250Ft-b4HB3MA-8 RC_T24099_at 3′. Yh16a10.s1 Homo sapiens cDNA clone 37689 3′. RC_R59292_at Zd25e10.s1 Soares fetal heart NbHH19W Homo sapiens RC_W60582_at cDNA clone 341706 3′ similar to gb: M38188 OVARIAN GRANULOSA CELL 13.0 KD PROTEIN HGR74 (HUMAN);. Human 5-lipoxygenase activating protein (FLAP) gene M63262_at Yc89d05.s1 Homo sapiens cDNA clone 23443 3′. RC_R38678_at Zd29g01.r1 Soares fetal heart NbHH19W Homo sapiens W60268_at cDNA clone 342096 5′. Zx80d02.r1 Soares ovary tumor NbHOT Homo sapiens cDNA AA465016_at clone 810051 5′ similar to TR: G1020091 G1020091 NEUROPSIN.; contains element LTR3 repetitive element;. Yd83f04.s1 Homo sapiens cDNA clone 114847 3′. RC_T79842_at Zq56g08.s1 Stratagene neuroepithelium (#937231) Homo RC_AA206225_at sapiens cDNA clone 645662 3′. Zx37g02.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA449914_at cDNA clone 788690 3′. H. sapiens partial cDNA sequence; clone c-3bh08. RC_F10211_at zv41f05.s1 Soares ovary tumor NbHOT Homo sapiens cDNA RC_AA480109_r_at clone 756225 3′ similar to TR: G498729 G498729 ZINC FINGER PROTEIN;. zl72a06.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA053102_s_at clone 510130 3′. zw24b11.s1 Soares ovary tumor NbHOT Homo sapiens RC_AA434113_at cDNA clone 770205 3′ similar to contains element TAR1 repetitive element;. zw62c02.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA441791_at cDNA clone 774626 3′. yz42c02.s1 Homo sapiens cDNA clone 285698 3′. RC_N67583_at ye47b12.s1 Homo sapiens cDNA clone 120863 3′. RC_T96077_at Human mRNA for KIAA0318 gene, partial cds. AB002316_at ze10g07.s1 Soares fetal heart NbHH19W Homo sapiens RC_W96222_at cDNA clone 358620 3′. Human hemopoietic cell protein-tyrosine kinase (HCK) gene, M16591_s_at complete cds, clone lambda-a2/1a yz76b12.s1 Homo sapiens cDNA clone 288959 3′. RC_N59808_at H. sapiens partial cDNA sequence; clone c-39g09. RC_F10040_at zx62b09.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA461549_at cDNA clone 796025 3′. zd35d04.s1 Soares fetal heart NbHH19W Homo sapiens RC_W68683_at cDNA clone 342631 3′. zn20d05.s1 Stratagene neuroepithelium NT2RAMI 937234 RC_AA084640_at Homo sapiens cDNA clone 547977 3′. HUMGS0007858, Human Gene Signature, 3′-directed cDNA C01169_at sequence. ab04a05.s1 Stratagene fetal retina 937202 Homo sapiens RC_AA491465_at cDNA clone 839792 3′. zd41c07.s1 Soares fetal heart NbHH19W Homo sapiens RC_W67564_s_at cDNA clone 343212 3′. Human beta-1-adrenergic receptor mRNA, complete cds. J03019_s_at yu77b06.s1 Homo sapiens cDNA clone 239795 3′. RC_H80622_at yy15h06.s1 Homo sapiens cDNA clone 271355 3′. RC_N34686_at yg91d08.s1 Homo sapiens cDNA clone 40992 3′. RC_R56066_s_at EST71577 Homo sapiens cDNA 3′ end similar to None. RC_T34611_at zk15e12.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA031373_s_at cDNA clone 470638 3′. Human mRNA for spi-1 proto-oncogene X52056_at yz89g12.r1 Homo sapiens cDNA clone 290278 5′. N77564_at HUMGS0003713, Human Gene Signature, 3′-directed cDNA C01765_at sequence. ae32d03.s1 Gessler Wilms tumor Homo sapiens cDNA clone RC_AA496936_at 897509 3′. zk04e03.s1 Soares pregnant uterus NbHPU Homo sapiens RC_AA027103_at cDNA clone 469564 3′. yg32c11.s1 Homo sapiens cDNA clone 34089 3′. RC_R44131_at yz48f04.s1 Homo sapiens cDNA clone 286303 3′. RC_N67227_at ye52f03.s1 Homo sapiens cDNA clone 121373 3′. RC_T96677_at zo23g05.s1 Stratagene colon (#937204) Homo sapiens cDNA RC_AA134965_i_at clone 587768 3′. yd87d10.s1 Homo sapiens cDNA clone 115219 3′. RC_T86600_at zf51f03.s1 Soares retina N2b4HR Homo sapiens cDNA clone RC_AA054087_at 380477 3′. zv76b10.r1 Soares total fetus Nb2HF8 9w Homo sapiens AA444374_at cDNA 5′. ys04f01.s1 Homo sapiens cDNA clone 213817 3′ similar to RC_H72357_at gb: J04970 CARBOXYPEPTIDASE M PRECURSOR (HUMAN); contains Alu repetitive element;. ze37d11.s1 Soares retina N2b4HR Homo sapiens cDNA clone RC_AA017045_at 361173 3′. zi09c03.r1 Soares fetal liver spleen 1NFLS S1 Homo sapiens AA010324_at cDNA clone 430276 5′. zs38b09.s1 Soares NhHMPu S1 Homo sapiens cDNA clone RC_AA234743_at 687449 3′. zf20d06.s1 Soares fetal heart NbHH19W Homo sapiens RC_AA055892_at cDNA clone 377483 3′. zw89g02.s1 Soares total fetus Nb2HF8 9w Homo sapiens RC_AA446650_at cDNA clone 784178 3′. ys80e03.r1 Homo sapiens cDNA clone 221116 5′. H91747_s_at zu63c08.r1 Soares testis NHT Homo sapiens cDNA clone AA401510_s_at 742670 5′. zd31d10.s1 Soares fetal heart NbHH19W Homo sapiens RC_W61239_at cDNA clone 342259 3′.

In another embodiment the probes consists of the sequences identified above.

The hybridization may be tested in vitro at conditions corresponding to in vivo conditions. Typically, hybridization conditions are of low to moderate stringency. These conditions favour specific interactions between completely complementary sequences, but allow some non-specific interaction between less than perfectly matched sequences to occur as well. After hybridization, the nucleic acids can be “washed” under moderate or high conditions of stringency to dissociate duplexes that are bound together by some non-specific interaction (the nucleic acids that form these duplexes are thus not completely complementary).

As is known in the art, the optimal conditions for washing are determined empirically, often by gradually increasing the stringency. The parameters that can be changed to affect stringency include, primarily, temperature and salt concentration. In general, the lower the salt concentration and the higher the temperature the higher the stringency. Washing can be initiated at a low temperature (for example, room temperature) using a solution containing a salt concentration that is equivalent to or lower than that of the hybridization solution. Subsequent washing can be carried out using progressively warmer solutions having the same salt concentration. As alternatives, the salt concentration can be lowered and the temperature maintained in the washing step, or the salt concentration can be lowered and the temperature increased. Additional parameters can also be altered. For example, use of a destabilizing agent, such as formamide, alters the stringency conditions.

In reactions where nucleic acids are hybridized, the conditions used to achieve a given level of stringency will vary. There is not one set of conditions, for example, that will allow duplexes to form between all nucleic acids that are 85% identical to one another; hybridization also depends on unique features of each nucleic acid. The length of the sequence, the composition of the sequence (for example, the content of purine-like nucleotides versus the content of pyrimidine-like nucleotides) and the type of nucleic acid (for example, DNA or RNA) affect hybridization. An additional consideration is whether one of the nucleic acids is immobilized (for example on a filter).

An example of a progression from lower to higher stringency conditions is the following, where the salt content is given as the relative abundance of SSC (a salt solution containing sodium chloride and sodium citrate; 2×SSC is 10-fold more concentrated than 0.2×SSC). Nucleic acids are hybridized at 42° C. in 2×SSC/0.1% SDS (sodium dodecylsulfate; a detergent) and then washed in 0.2×SSC/0.1% SDS at room temperature (for conditions of low stringency); 0.2×SSC/0.1% SDS at 42° C. (for conditions of moderate stringency); and 0.1×SSC at 68° C. (for conditions of high stringency). Washing can be carried out using only one of the conditions given, or each of the conditions can be used (for example, washing for 10-15 minutes each in the order listed above). Any or all of the washes can be repeated. As mentioned above, optimal conditions will vary and can be determined empirically.

In another aspect a method of reducing tumoregeneicity relates to the use of antibodies against an expression product of a cell from the biological tissue. The antibodies may be produced by any suitable method, such as a method comprising the steps of

-   obtaining expression product(s) from at least one gene said gene     being expressed as defined above for oncogenes, -   immunising a mammal with said expression product(s) obtaining     antibodies against the expression product.     Use

The methods described above may be used for producing an assay for diagnosing a biological condition in animal tissue, or for identification of the origin of a piece of tissue. Further, the methods of the invention may be used for prediction of a disease course and treatment response.

Furthermore, the invention relates to the use of a peptide as defined above for preparation of a pharmaceutical composition for the treatment of a biological condition in animal tissue.

Furthermore, the invention relates to the use of a gene as defined above for preparation of a pharmaceutical composition for the treatment of a biological condition in animal tissue.

Also, the invention relates to the use of a probe as defined above for preparation of a pharmaceutical composition for the treatment of a biological condition in animal tissue.

Gene Delivery Therapy

The genetic material discussed above for may be any of the described genes or functional parts thereof. The constructs may be introduced as a single DNA molecule encoding all of the genes, or different DNA molecules having one or more genes. The constructs may be introduced simultaneously or consecutively, each with the same or different markers.

The gene may be linked to the complex as such or protected by any suitable system normally used for transfection such as viral vectors or artificial viral envelope, liposomes or micellas, wherein the system is linked to the complex.

Numerous techniques for introducing DNA into eukaryotic cells are known to the skilled artisan. Often this is done by means of vectors, and often in the form of nucleic acid encapsidated by a (frequently virus-like) proteinaceous coat. Gene delivery systems may be applied to a wide range of clinical as well as experimental applications.

Vectors containing useful elements such as selectable and/or amplifiable markers, promoter/enhancer elements for expression in mammalian, particularly human, cells, and which may be used to prepare stocks of construct DNAs and for carrying out transfections are well known in the art. Many are commercially available.

Various techniques have been developed for modification of target tissue and cells in vivo. A number of virus vectors, discussed below, are known which allow transfection and random integration of the virus into the host. See, for example, Dubensky et al. (1984) Proc. Natl. Acad. Sci. USA 81:7529-7533; Kaneda et al., (1989) Science 243:375-378; Hiebert et al. (1989) Proc. Natl. Acad. Sci. USA 86:3594-3598; Hatzoglu et al., (1990) J. Biol. Chem. 265:17285-17293; Ferry et al. (1991) Proc. Natl. Acad. Sci. USA 88:8377-8381. Routes and modes of administering the vector include injection, e.g intravascularly or intramuscularly, inhalation, or other parenteral administration.

Advantages of adenovirus vectors for human gene therapy include the fact that recombination is rare, no human malignancies are known to be associated with such viruses, the adenovirus genome is double stranded DNA which can be manipulated to accept foreign genes of up to 7.5 kb in size, and live adenovirus is a safe human vaccine organisms.

Another vector which can express the DNA molecule of the present invention, and is useful in gene therapy, particularly in humans, is vaccinia virus, which can be rendered non-replicating (U.S. Pat. Nos. 5,225,336; 5,204,243; 5,155,020; 4,769,330).

Based on the concept of viral mimicry, artificial viral envelopes (AVE) are designed based on the structure and composition of a viral membrane, such as HIV-1 or RSV and used to deliver genes into cells in vitro and in vivo. See, for example, U.S. Pat. No. 5,252,348, Schreier H. et al., J. Mol. Recognit., 1995, 8:59-62; Schreier H et al., J. Biol. Chem., 1994, 269:9090-9098; Schreier, H., Pharm. Acta Helv. 1994, 68:145-159; Chander, R et al. Life Sci., 1992, 50:481-489, which references are hereby incorporated by reference in their entirety. The envelope is preferably produced in a two-step dialysis procedure where the “naked” envelope is formed initially, followed by unidirectional insertion of the viral surface glycoprotein of interest. This process and the physical characteristics of the resulting AVE are described in detail by Chander et al., (supra). Examples of AVE systems are (a) an AVE containing the HIV-1 surface glycoprotein gp160 (Chander et al., supra; Schreier et al., 1995, supra) or glycosyl phosphatidylinositol (GPI)-linked gp120 (Schreier et al., 1994, supra), respectively, and (b) an AVE containing the respiratory syncytial virus (RSV) attachment (G) and fusion (F) glycoproteins (Stecenko, A. A. et al., Pharm. Pharmacol. Left. 1:127-129 (1992)). Thus, vesicles are constructed which mimic the natural membranes of enveloped viruses in their ability to bind to and deliver materials to cells bearing corresponding surface receptors.

AVEs are used to deliver genes both by intravenous injection and by instillation in the lungs. For example, AVEs are manufactured to mimic RSV, exhibiting the RSV F surface glycoprotein which provides selective entry into epithelial cells. F-AVE are loaded with a plasmid coding for the gene of interest, (or a reporter gene such as CAT not present in mammalian tissue).

The AVE system described herein in physically and chemically essentially identical to the natural virus yet is entirely “artificial”, as it is constructed from phospholipids, cholesterol, and recombinant viral surface glycoproteins. Hence, there is no carry-over of viral genetic information and no danger of inadvertant viral infection. Construction of the AVEs in two independent steps allows for bulk production of the plain lipid envelopes which, in a separate second step, can then be marked with the desired viral glycoprotein, also allowing for the preparation of protein cocktail formulations if desired.

Another delivery vehicle for use in the present invention are based on the recent description of attenuated Shigella as a DNA delivery system (Sizemore, D. R. et al., Science 270:299-302 (1995), which reference is incorporated by reference in its entirety). This approach exploits the ability of Shigellae to enter epithelial cells and escape the phagocytic vacuole as a method for delivering the gene construct into the cytoplasm of the target cell. Invasion with as few as one to five bacteria can result in expression of the foreign plasmid DNA delivered by these bacteria.

A preferred type of mediator of nonviral transfection in vitro and in vivo is cationic (ammonium derivatized) lipids. These positively charged lipids form complexes with negatively charged DNA, resulting in DNA charged neutralization and compaction. The complexes endocytosed upon association with the cell membrane, and the DNA somehow escapes the endosome, gaining access to the cytoplasm. Cationic lipid:DNA complexes appear highly stable under normal conditions. Studies of the cationic lipid DOTAP suggest the complex dissociates when the inner layer of the cell membrane is destabilized and anionic lipids from the inner layer displace DNA from the cationic lipid. Several cationic lipids are available commercially. Two of these, DMRI and DC-cholesterol, have been used in human clinical trials. First generation cationic lipids are less efficient than viral vectors. For delivery to lung, any inflammatory responses accompanying the liposome administration are reduced by changing the delivery mode to aerosol administration which distributes the dose more evenly.

Drug Screening

Genes identified as changing in various stages of bladder cancer can be used as markers for drug screening. Thus by treating bladder cancer cells with test compounds or extracts, and monitoring the expression of genes identified as changing in the progression of bladder cancers, one can identify compounds or extracts which change expression of genes to a pattern which is of an earlier stage or even of normal bladder mucosa.

It is also within the scope of the invention to use small molecules in drug screening.

The following are non-limiting examples illustrating the present invention.

Experimentals

Affymetrix GeneChip Expression Analysis cRNA Preparation

10 μg total RNA was used as starting material for the cDNA preparation. The first and second strand cDNA synthesis was performed using the SuperScript Choice System (Life Technologies) according to the manufacturers instructions except using a oligo-dT primer containing a T7 RNA polymerase promoter site. Labeled cRNA was prepared using the BioArray High Yield RNA Transcript Labeling Kit (ENZO). Biotin labeled CTP and UTP (Enzo) were used in the reaction together with unlabeled NTP's. Following the IVT reaction, the unincorporated nucleotides were removed using RNeasy columns (Qiagen).

Array Hybridization and Scanning

Fifteen μg of cRNA was fragmented at 94° C. for 35 min in a fragmentation buffer containing 40 mM Tris-acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc. Prior to hybridization, the fragmented cRNA in a 6×SSPE-T hybridization buffer (1 M NaCl, 10 mM Tris pH 7.6, 0.005% Triton), was heated to 95° C. for 5 min and subsequently to 40° C. for 5 min before loading onto the Affymetrix probe array cartridge. The probe array was then incubated for 16 h at 45° C. at constant rotation (60 rpm). The washing and staining procedure was performed in the Affymetrix Fluidics Station. The probe array was exposed to 10 washes in 6×SSPE-T at 25° C. followed by 4 washes in 0.5×SSPE-T at 50° C. The biotinylated cRNA was stained with a streptavidin-phycoerythrin conjugate, final concentration 2 μg/μl (Molecular Probes, Eugene, Oreg.) in 6×SSPE-T for 30 min at 25° C. followed by 10 washes in 6×SSPE-T at 25° C. An antibody amplification step was added using normal goat IgG final concentration 0.1 mg/ml (Sigma) and Anti-streptavidin antibody (goat) biotinylated final concentration 3 μg/ml. (Vector Laboratories). This was followed by a staining step with a streptavidin-phycoerythrin conjugate, final concentration 2 μg/μl (Molecular Probes, Eugene, Oreg.) in 6×SSPE-T for 30 min at 25° C. and 10 washes in 6×SSPE-T at 25° C.

The probe arrays were scanned at 560 nm using a confocal laser-scanning microscope with an argon ion laser as the excitation source, (Hewlett Packard GeneArray Scanner G2500A). The readings from the quantitative scanning were analysed by the Affymetrix Gene Expression Analysis Software. For comparison from array to array, these were scaled to a global intensity of 150, as previously published (Zhu, H., Cong, J. P., Mamtora, G., Gingeras, T., and Shenk, T. Cellular gene expression altered by human cytomegalovirus: Global monitoring with oligonucleotide arrays. Proc. Natl Acad USA, 95:14470-75,1998).

A spreadsheat approach using the fold change of gene level and the scoring of presence or absence of genes was used to sort genes in the different categories.

Western Blotting Analysis

Ten μl diluted protein marker (ECL protein molecular marker, Amersham) were used. The samples were electrophoresed at 200 V for 50 min in an X-CELL system (Novex). Then the proteins were transferred to a PVDF membrane at 30 V for 1 hour followed by blocking for 1 hour. The membrane was subsequently washed in 3×10 min in PBS buffer pH 7.4+0.1% Tween 20. The membrane was incubated with polyclonal antibodies, against peptides derived from two genes with accession numbers Z40715 and AA116036, overnight at 4° C. The membrane was then washed 3×10 min in PBS buffer pH 7.4+0.1% Tween 20, followed by incubation for 1 hour with a biotinylated streptavidin horseradish peroxidase complex. The detection reagent (ECL+Western blotting detection system, Amersham) was applied for 5 min. Finally, the membrane was wrapped in plastic, sealed, and scanned in a Phosphorimager, STORM 840 (Molecular Dynamics, Amersham Pharmacia, Sweden).

Quantitative PCR Analysis Using Light Cycler (Roche™).

Quantitative PCR analysis was performed as described in the manufacturers instructions and as described in (Morrison et al (1998) Biotechniques 24 (6):954-962.). The quantitation was in all cases related to GAPDH. Ten samples was used in the quantitation experiment: Four T2-4 bladder tumor samples, four Ta bladder tumor samples, and two normal bladder samples.

For verification of expression levels by another method quantitative PCR based on a light cycler was made on three genes using Normal, Ta and T2 biopsy material. RNA was amplified and the data shown in the table below (Table XX) were obtained. It shows that a similar finding as made with the arrays were made using the light cycler. Genes that varied between normal and tumor samples and between tumor samples were reproduced by this independent method, showing the validity of the data. Due to the high number of genes only a few were selected for this reproducibility study, as a proof of principle.

Quantitative PCR analysis Category GeneChip: Upregulated in Upregulated in Upregulated in tumor Invasive tumors tumor Accession #: AA101562 AA417030 H20264 RNA Relative Relative Relative samples expression expression expression T2-4 #1 5.3 24.8 0 T2-4 #2 12.0 30.5 5.8 T2-4 #3 1.0 63.8 0.8 T2-4 #4 12.1 6.8 4.8 Ta #1 4.8 14.2 6.8 Ta #2 6.1 21.7 5.4 Ta #3 7.7 2.2 0.9 Ta #4 9.8 9.0 2.4 Normal #1 Absent Absent Absent Normal #2 Absent Absent Absent Average T2-4 7.6 31.5 2.9 Average Ta 7.1 11.7 3.9 Average Normal Absent Absent Absent

To correlate between RNA levels and protein levels western blots based on antibodies raised against synthetic peptides selected from the EST sequence was a performed (see FIG. 18). This was done with two EST's and the resulting two antibodies were used for western blotting of solubilized Normal, stage Ta and stage T2 bladder tumors. The experiment showed that similar findings were made using this protein apporoach. The level of proteins was much higher and more consistent in the tumor tissue than in the normal tissue, often being absent from normal tissue. Due to the high number of EST's only two were selected for this antibody based verification of the proteins (see FIG. 18). It should be regarded as a proof of principle. 

1. A method of classifying the disease course of a human bladder cancer tissue, comprising collecting a sample comprising cells from the cancer tissue, assaying the expression of at least one Ta stage gene from a Ta stage gene group, wherein said Ta gene is characterized by being up-regulated in Ta stage tissue compared to T2 stage tissue, and assaying at least one T2 stage gene from a T2 stage gene group, wherein said T2 gene is characterized by being up-regulated in T2 stage tissue compared to Ta stage tissue, wherein said Ta stage gene is SEQ ID NO: 1 and wherein said T2 stage gene is SEQ ID NO: 2, (i) correlating the expression level of the assessed Ta stage gene to a standard level of the Ta gene expression level in T2 stage tissue and (ii) correlating the expression level of the assessed T2 stage gene to a standard level of the T2 gene expression level in Ta stage tissue, wherein up-regulation of the expression level of said Ta stage gene and down-regulation of said T2 stage gene classifies said bladder cancer disease course as non-muscle invasive and wherein up-regulation of the expression level of said T2 stage gene and down-regulation of said Ta stage gene classifies said bladder cancer disease course as muscle invasive.
 2. A method of classifying the disease course of a human bladder cancer tissue, comprising collecting a sample comprising cells from the cancer tissue, assaying the expression of at least one Ta stage gene from a Ta stage gene group, wherein said Ta gene is characterized by being up-regulated in Ta stage tissue compared to T2 stage tissue, and assaying at least one T2 stage gene from a T2 stage gene group, wherein said T2 gene is characterized by being up-regulated in T2 stage tissue compared to Ta stage tissue, wherein said Ta stage gene comprises the sequence of SEQ ID NO: 1 and wherein said T2 gene comprises the sequence of SEQ ID NO: 2, (i) correlating the expression level of the assessed Ta stage gene to a standard level of the Ta gene expression level in T2 stage tissue and (ii) correlating the expression level of the assessed T2 stage gene to a standard level of the T2 gene expression level in Ta stage tissue, wherein up-regulation of the expression level of said Ta stage gene and down-regulation of said T2 stage gene classifies said bladder cancer disease course as non-muscle invasive and wherein up-regulation of the expression level of said T2 stage gene and down-regulation of said Ta stage gene classifies said bladder cancer disease course as muscle invasive. 